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Obsoleting an Existing Ontology Term

See Daily Workflow for creating branches and basic Protégé instructions.

Warning: Every ontology has their procedures on how they obsolete terms (eg notice periods, notification emails, to_be_obsolete tags, etc.), this how-to guide only serves as a guide on how obsolete a term directly on protege.

PRE OBSOLETION PROCESS (or basic obsoletion etiquette) 1. Check if the term (or any of its children) is being used for annotation: - Go to your ontology browser of choice, search for the term, either by label or ID - See which other ontologies use the to be obsolete term - Notify affected groups (usually by adding an issue in their tracker)

  1. Check if the term is used elsewhere in the ontology
  2. In Protégé, navigate to the term to be obsolete and go to the 'Usage' tab to see if that ID is used elsewhere.
  3. If the term is a parent to other terms or is used in logical definitions, make sure that another term replaces the obsolete term

OBSOLETION PROCESS (Manual)

  1. Navigate to the term to be obsoleted.

  2. Make the status of the term obsolete:

  3. In the 'Annotations' window, click on the + sign next to 'Annotations'.

  4. In the resulting pop-up window, select owl:deprecated from the left-hand menu.
  5. Make sure the 'Literal' tab view is selected from the right-hand tab list. Type true in the text box.
  6. In the 'Type' drop-down menu underneath the text box, select xsd:boolean
  7. Click OK. You should now see the term crossed out in the Class hierarchy view.

  8. Remove equivalence axiom: In the 'Description' window, under the 'Equivalent To', click the x on the right-hand side to delete the logical definition.

  9. Remove 'SubClass Of' relations: In the 'Description' window, under the 'SubClass Of' entry, click the x on the right-hand side to delete the SubClass Relation.

  10. Add ‘obsolete’ to the term name: In the 'Annotations' window, click on the o on the right-hand side of the rdfs:label entry to edit the term string. In the resulting window, in the Literal tab, in front of the term name, type: obsolete For example: obsolete gamma-glutamyltransferase activity Note the case-sensitivity. Make sure to have a space (and no other character) between 'obsolete' and the term label.

  11. Add ‘OBSOLETE’ to the term definition: In the 'Description' window, click on the o on the right-hand side of the definition entry. In the resulting window, in the Literal tab, at the beginning of the definition, type: OBSOLETE. For example: OBSOLETE. Catalysis of the reaction: (5-L-glutamyl)-peptide + an amino acid = peptide + 5-L-glutamyl-amino acid. Note the case-sensitivity.

  12. Add a statement about why the term was made obsolete: In the 'Annotations' window, select + to add an annotation. In the resulting menu, select rdfs:comment and select Type: Xsd:string. Consult the wiki documentation for suggestions on standard comments:

  13. If the obsoleted term was replaced by another term in the ontology: In the 'Annotations' window, select + to add an annotation. In the resulting menu, select term replaced by and enter the ID of the replacement term.

  14. If the obsoleted term was not replaced by another term in the ontology, but there are existing terms that might be appropriate for annotation, add those term IDs in the 'consider' tag: In the 'Annotations' window, select + to add an annotation. In the resulting menu, select consider and enter the ID of the replacement term.

  15. Save changes.

Obsolete a class (using Protege 'Make entity obsolete' function)

  1. Navigate to the term to be obsoleted.
  2. In the Protege edit menu-> Make entity obsolete
  3. Prepend the definition with OBSOLETE. For example, OBSOLETE. Chronic form of myeloproliferative neoplasm.
  4. Add a statement about why the term was made obsolete: In the 'Annotations' window, select + to add an annotation. In the resulting menu, select rdfs:comment and select Type: Xsd:string. Consult the wiki documentation for suggestions on standard comments:

  5. If the obsoleted term was replaced by another term in the ontology: In the 'Annotations' window, select + to add an annotation. In the resulting menu, select term replaced by and enter the ID of the replacement term.

  6. If the obsoleted term was not replaced by another term in the ontology, but there are existing terms that might be appropriate for annotation, add those term IDs in the 'consider' tag: In the 'Annotations' window, select + to add an annotation. In the resulting menu, select consider and enter the ID of the replacement term.

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