Protege5 6 setup for GO Eds

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About this documentation

These instructions were done on Mac OS.

Protege version

As of March 2023, GO Ontology Editors are using Protege version 5.6.1

Download and install Protege

  • Get Protege from its GitHub project site
    • Choose the .zip or .tar.gz download specific to your platform: os-x (Mac), win (Windows), or linux (Linux).
  • Unzip and move the Protege app to your Applications folder.
  • The first time you try to run the Protégé.app, you will get a warning:

    Press Cancel to close the warning. Right-click (or Control-click) on Protégé.app and select Open. You will then see a different warning:

    Press Open, and Protege should launch. For subsequent launches you should be able to simply double-click Protégé.app to open it without warnings.
  • See Install_Protege5_Mac for more instructions and troubleshooting common problems, but keep in mind that some details may have changed since that page was updated.

Fix memory settings

Protege needs at least 4G of RAM to cope with the GO, ideally use 12G or 16G if your machine can handle it.

  • If running from Protege.app on a Mac, open the /Applications/Protégé.app/Contents/conf/jvm.conf or /Applications/Protege-5.6.0/Protégé.app/Contents/conf/jvm.conf file using a text editor
    • Uncomment the line: #max_heap_size=8G (remove the #)
    • Replace 8 with the number of gigabytes of memory you would like to provide to Protege (ideally not more than 75% of your system memory total): max_heap_size=16G

Instructions for new Protege users

Obtaining your ID range

  • Curators and projects are assigned specific GO term ID ranges by senior editors.
  • These ID ranges are stored in the file: [1]
  • NOTE: You should only use IDs within your range.

Setting ID range

  • As of version 5.6.0, Protege automatically reads the go-idranges.owl file.
    • When you open go-edit.obo, Protege will open a panel asking you to select the ID range entry you will be using (select your own name).
    • If there is an entry in go-idranges.owl file that exactly matches your computer login username, that range will be automatically selected and you will not be prompted.
  • The built-in ID ranges support should allow you to smoothly switch between editing GO and editing another OBO library ontology, without reconfiguring ID generation, but there is a bug in Protege 5.6.1 in which the ID range must be manually set when working in different ontologies.

Setting username and auto-adding creation date

  1. In the Protege menu, go to Preferences > New Entities Metadata tab
  2. Check Annotate new entities with creator (user) box
  3. Creator property Add http://www.geneontology.org/formats/oboInOwl#created_by
  4. Creator value Select Use user name
  5. Check Annotate new entities with creation date/time box
  6. Date property Add http://www.geneontology.org/formats/oboInOwl#creation_date
  7. Date value format Select ISO-8601

Configuring User details

  • In the Protege menu, go to Preferences > User details
  • User nameSelect Use supplied user name, and use your GOC identity (see your 'xref' in users.yaml). Enter the initials following GO: in the users.yaml file.

Setting Rendering

(The default settings may be fine, but details are included for reference)

  • In the Protege menu, go to Preferences > Renderer

Protege allows users to set the annotation property to be used for rendering OWL entities (classes, object properties, annotation properties, individuals) in graphs, trees and text etc. This should be set to rdfs:label, as follows:

More on rendering. All entities in OWL are identified by an IRI (Internationalized Resource Identifier [2]). Entities also includes annotation properties such as human-readable labels. In the absence of an annotation to annotation property specified as suitable for rendering, the short form of this IRI (the bit following a '#' or a '/') is displayed. Choosing to render with rdfs:label displays term labels in Protege.

Viewing Obsolete Terms

Protege 5.6 hides deprecated (obsolete) terms by default. To view them, go to the View menu and select Display deprecated (obsolete) entities.

Configuring layout

Adding Views as Panels or as Tabs

  • Protege has a highly configurable layout and a plugin architecture. You can control which components are visible from the window menu. To insert a view, go to Windows > View > Select the view you want to insert in the Protege layout.
  • The mouse pointer will have a small black target icon above it.

Adding a view as a new panel

  • Mouse-over the window you want to add a new panel to, until you see a blue rectangle splitting the window approximately in half, and click to drop the panel there.

Adding a view as a new tab

  • Mouse-over the middle area of the window you want to add a new tab to, until you see a large blue rectangle covering the entire window to which you want to add a tab, and click to drop the window there.

The following tabs are sufficient for GO work:

  • Active ontology
  • Entities (which also contains tabs for object properties and annotation properties by default)
  • DL query

  • You can remove plugins by clicking on the arrow at the right of the plugin tab.
  • Once the layout is to your liking, go to Windows > Store current layout

Installing plugins

If some plugins are not available from the Window>Views tab, go to File Check for plugins. Note: this takes some time. You can see Protege running by looking at the top right corner for the spinning wheel. The plugin menu will appear, showing available plugins or newer versions of already installed plugins:

Note the checkbox 'Always check for updates on startup'. It is recommended that you uncheck this box, since this notably slows down launching Protege.

One plugin you may find useful to install is the OBO Taxon Constraints panel. Instructions are available on its site.

Protege 5.6.x new features

  • ELK 0.5 is now included in the download.
  • (Automatic ID ranges support - feature not working)

See Protege GitHub release notes

Review Status

Last reviewed: January 9, 2024

Reviewed by: Pascale Gaudet

Previous review: Jim Balhoff, February 17, 2023

Back to: Ontology_Development