Setup Protege 5.5¶
These instructions are for Mac OS
As of July 2022, OBO ontology editors are using
Protege version 5.5.0
Download and install Protege¶
- Get Protege from protege.stanford.edu
- Unzip and move the Protege app to your Applications folder.
- See Install_Protege5_Mac for more instructions and troubleshooting common problems.
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.
- If running from Protege.app on a Mac, open the /Applications/Protege-5.5.0/Protégé.app/Contents/info.plist file
- Below the line:
- Insert another line:
Some Mac users might find that the edits need to be applied to
adapted from Memory Management with Protégé by Michael DeBellis
- Navigate to folder where Protege is installed (likely c:/programfiles/protege or open explorer and search protege.exe and find the location of file)
- 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
- 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.
- Change -Xmx500M to Xmx12G
- 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.
Use supplied user name:add your name (ie nicolevasilevsky)
Use Git user name when available
ORCID. Add the ID number only, do not include https://, ie 0000-0001-5208-3432
Setting username and auto-adding creation date¶
- In the Protege menu, go to
New Entities Metadatatab
Annotate new entities with creator (user)box
Creator propertyAdd http://www.geneontology.org/formats/oboInOwl#created_by
Creator valueSelect Use ORCID
Date value formatSelect 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:
- Go to
File > Check for plugins....
- Click on
OBO Annotations Editorand click on
- Restart Protege for the plugin to be active.
- You should now have the option to obsolete entities in
Edit > Make entity obsolete.
- You can see a list of all installed plugins in
Preferences > Plugins.