diff --git a/principles/fp-019-term-stability.md b/principles/fp-019-term-stability.md index 4869789ea..cd24cd5bf 100644 --- a/principles/fp-019-term-stability.md +++ b/principles/fp-019-term-stability.md @@ -46,23 +46,30 @@ It is not necessary (and not advisable) to delete the textual definition. To obsolete a term, the ontology developer SHOULD: 1) Indicate any exact term replacement: - - OWL: Use the "term replaced by" annotation property from OMO ([IAO:0100001](http://purl.obolibrary.org/obo/IAO_0100001)) with the value set to the IRI of the relevant term - - OBO: Use the "replaced_by:" tag with the value set to the CURIE of the relevant term + - OWL: Use the "term replaced by" annotation property from OMO ([IAO:0100001](http://purl.obolibrary.org/obo/IAO_0100001)) with the value set to the IRI of the relevant term + - OBO: Use the "replaced_by:" tag with the value set to the CURIE of the relevant term 2) Indicate any inexact term replacements: - - OWL: Use the "oboInOwl:consider" annotation property with the value set either to the full IRI(s) or to the CURIE(s) of the relevant term(s) + - OWL: Use the "oboInOwl:consider" annotation property with the value set to the full IRI(s) of the relevant term(s) ``` - IRI method: OBI:0001544 + ``` - - OBO: Use the "consider:" tag with the value set to the CURIE(s) of the relevant term(s) + - OBO: Use the "consider:" tag with the value set to the CURIE(s) of the relevant term(s) +``` + consider: OBI:0001544 +``` + +Note that some older implementations in OWL used the CURIE method as shown below, but this is not preferred. +``` + OBI:0001544 +``` To obsolete a term, the ontology developer MAY: 1) Prepend the string "OBSOLETE. " (this precise string, including the space) to the term definition. NOTE: This MUST be implemented consistently. That is, if applied at all, it has to be applied to every obsoleted term definition. 2) Indicate the reason(s) for obsoleting: - - OWL: Use the "has obsolescence reason" annotation property from OMO ([IAO:0000231](http://purl.obolibrary.org/obo/IAO_0000231)) with the value set to the IRI of one of the individuals of the "obsolescence reason specification" term [IAO:0000225](http://purl.obolibrary.org/obo/IAO_0000225) - - OBO: Use "property_value:" with the CURIE for the annotation property (IAO:0000231) and a CURIE for the specific reason (an individual from the "obsolescence reason specification" term [IAO:0000225](http://purl.obolibrary.org/obo/IAO_0000225)). See alternative methods below. + - OWL: Use the "has obsolescence reason" annotation property from OMO ([IAO:0000231](http://purl.obolibrary.org/obo/IAO_0000231)) with the value set to the IRI of one of the individuals of the "obsolescence reason specification" term [IAO:0000225](http://purl.obolibrary.org/obo/IAO_0000225). See below for example. + - OBO: Use "relationship:" with the CURIE for the annotation property (IAO:0000231) and a CURIE for the specific reason (an individual from the "obsolescence reason specification" term [IAO:0000225](http://purl.obolibrary.org/obo/IAO_0000225)). See below for example. Note that older implementations often used alternative methods (described after the examples). These methods are still valid, but are not preferred. Examples ------- @@ -87,12 +94,13 @@ OBO: id: OBI:0001574 name: obsolete cell lysate MHC competitive binding assay using radioactivity detection def: "OBSOLETE. Competitive inhibition of binding assay measuring MHC ligand binding by radioactivity detection using MHC derived from a cell lysate." [] -property_value: IAO:0000231 IAO:0000227 +relationship: IAO:0000231 IAO:0000227 is_obsolete: true replaced_by: OBI:0001544 ``` For OBO format, there are multiple alternatives: -1) Use "relationship:" instead of "property_value:". +1) Use "property_value:" instead of "relationship:". +1) Use a free text "comment:". 1) Use the annotation property label (with underscores) instead of the CURIE "IAO:0000231", and the obsolescence reason label instead of the relevant CURIE. Note that the underscore version of the property label will need to be created in the ontology: ``` [Typedef]