Protégé 5.5.0-beta-3 available

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Protégé 5.5.0-beta-3 available

Matthew Horridge-2
Administrator
Dear Protégé Users,

We are pleased to announce the release of Protégé 5.5.0-beta-3

The release is available for download at https://protege.stanford.edu/products.php#desktop-protege

The main features of Protégé 5.5.0 are:

Mixed hierarchies.  Protege now has 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 the Protégé user community.

fig-mixed-hierarchy

New breadcrumb trail.  We’ve 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


Lightweight Git integration support. When opening ontologies that are contained in a git repository, the current git branch will be displayed in the status bar.

fig-git-repo-status

It is also possible to use your git user name for createdBy annotation in Protege

fig-git-user-name


Improved display of OBO Ids.  We have improved the various tool tips and search results to display OBO Ids if present.  Hovering over entity names displays the OBO Id for that entity, if it is present.

fig-search


Extended Copy Actions.  We’ve added a popup menu to the entity header that contains useful actions for the selected entity

fig-term-header

Entity Deprecation Wizard.  We have 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.

Please try out this beta release and let us have your feedback.

Acknowledgements

We’d like to take this opportunity to thank all members of the Protégé User Community.  Many of the features that are included in Protégé 5.5.0 (beta) are due to feedback and suggestions provided by members of the Biomedical Ontology Engineering Community.  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. 

Best regards,

The Protégé Team



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