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Protege 5.6 setup for Mondo Editors

(This was adopted from the Gene Ontology editors guide)

Operating system

These instructions are for Mac OS.

Protege version

As of August 2023, Mondo editors are using `Protege version 5.6.

Download and install Protege

ELK reasoner

The ELK reasoner is included with Protege 5.6. For instructions on adding the ELK reasoner (if you are using an older version of Protege), see the Install Elk 0.5 in Protege how to guide.

Increase memory in Protege

Starting from version 5.6, Protege will automatically set the maximal amount of memory it can use, based on how much memory is available on your system:

  • if you have less than 4G of RAM, Protege will use at most 1G;
  • if you have between 4 and 8G, Protege will use at most half of the system memory (e.g., 3G if you have 6G);
  • if you have between 8 and 16G, Protege will use at most two-thirds of the system memory (e.g., 8G if you have 12G);
  • if you have more than 16G, Protege will use at most 75% of the system memory (e.g., 18G if you have 24G).

This default behaviour means that in most cases, editors shouldn’t have to worry about manually setting Protege’s max available memory.

Should you wish anyway to set the maximal amount of memory to an explicit value, you may do so by editing the file .Protege/conf/jvm.conf in your home directory (create that file, and the parent directory .Protege/conf itself, if it does not already exist) and adding a line like the following:


where 20G is the maxinmal amount of memory you want Protege to use. Restart Protege (if it was already running) for the new setting to be taken into account.

When Protege is running, you can check how much memory it is configured to use by opening the “About Protege” dialog (Protege > About Protege). Look for the line “Max memory set to ...MB”.

Instructions for new Protege users

Obtaining your ID range

  • Curators and projects are assigned specific Mondo term ID ranges by senior editors.
  • These ID ranges are stored in the file: mondo-idranges.owl
  • NOTE: You should only use IDs within your range.

Setting ID range

Protégé 5.6 can now automatically set up the ID range for a given user by exploiting the idranges.owl file, if it exists.

This Protege version looks at the ID range file and matches your user name in Protege to the names in the file to automatically set up your ID range. Thus as long as this information matches you no longer need to manually set the ID range. You will get a message if your user name does not match one in the file asking you to pick an ID range.

Note: If you are switching from an old Protege version to Protege 5.6, you may need to reset your range to the last used ID rather than just the full range or Protege would try to fill in gaps in the range.

If you are using an older version of Protege, see the instructions on setting the ID range in OBO Academy.)

Switching ID range

Protege 5.6 manages ID ranges for you automatically and these instructions are not needed.

If you are you using an older version of Protege, see the instructions here.

User details

  1. User name Clcik 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. In the Creator property field, add
  4. Creator value Select Use ORCID
  5. Date property
  6. Date value format Select ISO-8601