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@csnyulas csnyulas released this Mar 14, 2019 · 2 commits to master since this release

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.

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.
Assets 6

@matthewhorridge matthewhorridge released this Feb 7, 2019 · 5 commits to master since this release

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. image

  • 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. image

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

Assets 6

@matthewhorridge matthewhorridge released this Jan 15, 2019 · 5 commits to master since this release

Protégé 5.5.0-beta-8

This release fixes a problem that prevented some installations from displaying Chinese Characters

Assets 6

@matthewhorridge matthewhorridge released this Dec 18, 2018 · 6 commits to master since this release

Protégé 5.5.0-beta-7

This is a bug fix release.

Bug Fixes

  • Fixed a problem that could cause Protégé to hang when loading imported ontologies in some circumstances (Protégé 5.5.0-beta-7)
  • Fixed a problem that could cause the SPARQL Query Tab to crash when loading
Assets 6

@csnyulas csnyulas released this Nov 8, 2018 · 10 commits to master since this release

This 5.5.0-beta-5 release fixes one critical bug causing NullPointerExceptions to be thrown during certain searches: protegeproject/protege#813

Assets 6

@matthewhorridge matthewhorridge released this Oct 23, 2018 · 10 commits to master since this release

This 5.5.0-beta-4 release fixes some bugs and improves the log view user interface.

UI Improvements

The log view is now more scalable and customisable. 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 improvements.

Bug fixes

  • 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
Assets 6

@matthewhorridge matthewhorridge released this Sep 19, 2018 · 12 commits to master since this release

This beta-3 release updates the OWL API to version 4.5.6. In addition to this, the following features are carried over from 5.5.0-beta-2:

  • 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 createdBy annotation in Protege

fig-git-repo-status

fig-git-user-name

  • Improved the various tool tips and search results to display OBO Ids if present

fig-search

  • Added a popup menu to the entity header that contains useful actions for the selected entity.

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.

  • Improved rendering performance for large hierarchies

Assets 6

@matthewhorridge matthewhorridge released this Mar 15, 2017 · 18 commits to master since this release

This release contains various enhancements and fixes. Please note that if you are running MacOS Sierra then you may have to take some steps to enable the native Protege application to run.

Improvements & Enhancements

Context Sensitive Help

  • We have added context sensitive help to many of the views in Protégé. If help is available for a view then that help can be shown by pressing the "question mark" button in the view header. Help documentation ultimately points to here.

    (protegeproject/protege#587)

  • We have also added help documentation for the class expression syntax that is used in Protege. The help documentation can be displayed via the help button on the class expression editor dialog. Documentation can be found here.

    (protegeproject/protege#592 and protegeproject/protege#593)

Entities Tab Improvements

  • PubMed Ids in annotations that contain white space are now parsed and displayed as links to PubMed (protegeproject/protege#615)
  • Anonymous individuals that are auto-created for use in annotation values are no longer prefixed with the ontology Id
  • Entity names in lists are no longer quoted with single quotes in order to improve readability.

General User Interface Improvements

Changes for Developers

Fixes

Assets 6

@matthewhorridge matthewhorridge released this Oct 11, 2016 · 20 commits to master since this release

This release contains various enhancements and fixes.

Improvements & Enhancements

Annotation Editing & Viewing

  • The annotation value editor now indicates whether or not the entered value is in the lexical space of the selected datatype. For example, if the entered value was “Hello” but the datatype is specified as xsd:integer then an error message will be displayed. (protegeproject/protege#441)
  • Annotation values that are anonymous individuals now have property assertions that the individual is a subject of displayed inline. (protegeproject/protege#443)
  • Added usage of IRIs that are annotation values and correspond to entity IRIs to the kinds of usage displayed in the usage view. (protegeproject/protege#483)
  • Annotation values that correspond to PubMed Ids are now shown as hyperlinks. When clicked a new browser window is opened and the corresponding Id is displayed on the PubMed Website. (protegeproject/protege#512)

linked-annotations

  • ISBNs in annotation values are now shown as hyperlinks. Clicking one of these links opens a new window displaying information about the ISBN. (protegeproject/protege#513)
  • Wikipedia identifiers such as wikipedia:Cell that appear in annotation values are now shown as hyperlinks. Clicking such a link will open a browser window and display the relevant Wikipedia page. (protegeproject/protege#515)
  • Improved the scrolling behaviour of annotation views when annotation values with large amounts of text are displayed. (protegeproject/protege#516)
  • Changed the behaviour of the annotation value editor so that it focuses the actual editor when it is displayed. Previously, the annotation property list on the left hand side was focuses on open. (protegeproject/protege#537)

Entities Tab Improvements

  • Changed the default layout of the Entities tab so that the left hand side is more spacious and so that it is clearer as to what is selected. Note that users who wish to see these changes should reset the layout of the Entities tab by selecting “Window” -> “Reset selected tab to default state”(protegeproject/protege#504)
  • Improved the selection mechanism in the Protege User Interface. Switching a view that drives the selection (such as a tree) now causes the selection to be updated without having to reselect the entity in the tree. (protegeproject/protege#506 and protegeproject/protege#335)
  • Changed the behaviour of the Entities tab so that the right hand side now indicates if there isn’t any entity selected. (protegeproject/protege#507)
  • The right hand side entities tab nows displays the IRI for the selected entity (protegeproject/protege#525)

iri-example

General User Interface Improvements

Other Changes

Changes for Developers

Fixes

Updates to Plugins

  • Updated the DL Query Tab to version 4.0.1
  • Updated Cellfie to 2.1.0. You can find detailed release notes here.

Assets 6
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