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Setup Protege 5.5

(This was adopted from the Gene Ontology editors guide and Mondo documentation)

Operating System

These instructions are for Mac OS

Protege version

As of July 2022, OBO ontology editors are using Protege version 5.5.0

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.

Mac Instructions

  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

adapted from Memory Management with Protégé by Michael DeBellis

  1. Navigate to folder where Protege is installed (likely c:/programfiles/protege or open explorer and search protege.exe and find the location of file)
  2. Open Protege.l4j.ini. This file is what Protege looks at when it starts up to determine how much memory Java can allocate. If you edit that file in Notepad or some other lightweight text processor it should currently look like this: -Xms200M -Xmx500M -Xss16M
  3. Xmx is the one you want to edit (it is recommended that you make a copy of the original file first). That specifies the maximum amount of memory Protege can use. Xms is the initial memory that will be allocated and Xss defines the increments used when allocating more memory.
  4. Change -Xmx500M to Xmx12G
  5. Save and reopen Protege.

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.