Adding and Removing GO Subsets (Slims)

See Ontology_Editors_Daily_Workflow for creating branches and basic Protégé instructions.

Adding a new subset

1. In the main Protege window, click on the Annotation Properties tab.
2. Navigate to the subset_property and select it.
3. Click on the top left-hand button of the window to add a new subset property.
4. In the pop-up window add the name of the new slim. The identifier will fill in according to your preferences and will be the next GO identifier in your set. Click on Refactor in the menu. Select rename entities.
5. Replace the GO_ identifier with the name of your new slim. It is standard to use the same string as when you created the term.
6. In the annotations tab, click on the +.
7. In the pop up window, select rdfs:comment.
8. In the right hand window, type a small descriptor statement for the slim. Select xsd:string as the type.
9. Click OK to save the changes. You should now see the comment field in the annotations tab.
10. Add a task on the corresponding ticket to edit the Makefile to add the subset.

Removing a subset

1. Navigate to the subset by search on its name in the Search box.
2. Delete it by clicking on the x in the Annotation property panel.
3. Protege will give a message: Delete [ subset name ]? All references to [ subset name ] will be removed from the active ontologies. Click OK.
4. Save.
5. Add a task on the corresponding ticket to edit the Makefile to remove the subset.
   You can make the change yourself, via PR, by editing PUBLISH_SUBSETS = gocheck_do_not_annotate goslim_agr goslim_candida goslim_chembl goslim_drosophila goslim_flybase_ribbon goslim_generic goslim_metagenomics goslim_mouse goslim_pir goslim_plant goslim_pombe goslim_synapse goslim_yeast goslim_prokaryote in https://github.com/geneontology/go-ontology/blob/master/src/ontology/Makefile .

 See Ontology_Editors_Daily_Workflow for commit, push and merge instructions.

Review Status

Last reviewed: March 15, 2024

Reviewed by Pascale Gaudet

Back to: Editing the Ontology