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Setup Protege 5.5

(This was adopted from the Gene Ontology editors guide and Mondo documentation). Updated 2023-01-20 by Nicole Vasilevsky

Mac Instructions

These instructions are for Mac OS

Protege version

As of July 2022, OBO ontology editors are using Protege version 5.5.0. A new beta version is currently out and available for testing.

Download and install Protege

Increase memory in Protege

Protege needs at least 4G of RAM to cope with Mondo, ideally use 12G or 16G if your machine can handle it. Edits to the Protege configuration files will not take effect until Protege is restarted.

  1. If running from Protege.app on a Mac, open the /Applications/Protege-5.5.0/Protégé.app/Contents/info.plist file
  2. Below the line: <string>-Xss16M</string>
  3. Insert another line: <string>-Xmx12G</string>

Some Mac users might find that the edits need to be applied to /Applications/Protégé.app/Contents/Info.plist.

PC Instructions

Taken in part from Memory Management with Protégé by Michael DeBellis. Updated by Nicole Vasilevsky.

The following instructions will probably not work if Protégé was installed from the platform independent version, which does not include the Java Runtime Environment or a Windows .exe launcher.

  • Visit https://protege.stanford.edu/
  • Click orange DOWNLOAD NOW button
  • Click gray Download for Windows button on subsequent page
  • Register if desired, or skip registration
  • Find Protege-<version>-win.zip
  • most likely in your Downloads directory (or in This PC directory)
  • current version is Protege-5.5.0-win.zip
  • Unzip the downloaded file with your favorite file compression utility
  • You should see the Protege application and a file called 'run'
  • To open Protege, double-click the 'run' file. This will open cmd.exe and it will take a bit to open the file.
  • The fonts used by Protégé may be very small, especially on some high resolution monitors. To increase the font size, go to File -> Preferences -> Renderer -> Font size.
  • Exit Protégé after confirming that it can be launched.
  • There should be a Protege.l4j.ini in the same directory as Protege.exe. Opening large ontologies like MONDO will require an increase to Protege's default maximum Java heap size, which is symbolized as -Xmx<size>. 4GB is usually adequate for opening MONDO, as long as 4GB of free memory is really available on your system before you launch Protégé! Allocating even more memory will improve some tasks, like reasoning. You can check your available memory by launching the Windows Task Manager, clicking on the More details button on the bottom of the window and then checking the Performance tab at the top of the window.
  • It's recommended to make a backup of Protege.l4j.ini before editing

Open Protege.l4j.ini with a lightweight text editor like Atom or Sublime. Using notepad.exe instead might work, but may change character encodings or the character(s) used to represent End of Line.

After increasing the memory available to Protégé, Protege.l4j.ini might look like this.

-Xms200M
-Xmx4G
-Xss16M

Note that there is no whitespace between -Xmx, the numerical amount of memory, and the Megabytes/Gigabytes suffix. Don't forget to save.

Taking advantage of the memory increase requires that Protégé is shut down and relaunched, if applicable. The methods discussed here may not apply if Protégé is launched through any method other than double clicking Protege.exe from the folder where the edited Protege.l4j.ini resides.

Note on increasing memory

If you have issues opening Protege, then reduce the memory, try 10G (or lower) instead.

Add ELK reasoner

See instructions here.

Instructions for new Protege users

Setting your ID range

See instructions here.

User details

  1. User name Click Use supplied user name: add your name (ie nicolevasilevsky)
  2. Check Use Git user name when available
  3. Add ORCID. Add the ID number only, do not include https://, ie 0000-0001-5208-3432

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 ORCID
  5. Date property http://purl.org/dc/elements/1.1/date
  6. Date value format Select ISO-8601

Install Protege OBO plugin

This plugin enables some extra functionality, such as the option to obsolete entities from the menu. To install it:

  1. Go to File > Check for plugins....
  2. Click on OBO Annotations Editor and click on Install.
  3. Restart Protege for the plugin to be active.
  4. You should now have the option to obsolete entities in Edit > Make entity obsolete.
  5. You can see a list of all installed plugins in Preferences > Plugins.