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Update fp-019-term-stability.md
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principles/fp-019-term-stability.md

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@@ -46,23 +46,30 @@ It is not necessary (and not advisable) to delete the textual definition.
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<i><b>To obsolete a term, the ontology developer</b></i> SHOULD:
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1) Indicate any exact term replacement:
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- 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
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- OBO: Use the "replaced_by:" tag with the value set to the CURIE of the relevant term
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- 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
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- OBO: Use the "replaced_by:" tag with the value set to the CURIE of the relevant term
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2) Indicate any inexact term replacements:
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- 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)
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- OWL: Use the "oboInOwl:consider" annotation property with the value set to the full IRI(s) of the relevant term(s)
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```
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IRI method: <oboInOwl:consider rdf:resource="http://purl.obolibrary.org/obo/OBI_0001544)>
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CURIE method: <oboInOwl:consider rdf:datatype="http://www.w3.org/2001/XMLSchema#string">OBI:0001544</oboInOwl:consider>
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<oboInOwl:consider rdf:resource="http://purl.obolibrary.org/obo/OBI_0001544")>
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```
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- OBO: Use the "consider:" tag with the value set to the CURIE(s) of the relevant term(s)
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- OBO: Use the "consider:" tag with the value set to the CURIE(s) of the relevant term(s)
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```
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consider: OBI:0001544
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```
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Note that some older implementations in OWL used the CURIE method as shown below, but this is not preferred.
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```
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<oboInOwl:consider rdf:datatype="http://www.w3.org/2001/XMLSchema#string">OBI:0001544</oboInOwl:consider>
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```
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<i><b>To obsolete a term, the ontology developer</b></i> MAY:
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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.
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2) Indicate the reason(s) for obsoleting:
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- 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)
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- 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.
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- 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.
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- 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.
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Examples
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-------
@@ -87,12 +94,13 @@ OBO:
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id: OBI:0001574
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name: obsolete cell lysate MHC competitive binding assay using radioactivity detection
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def: "OBSOLETE. Competitive inhibition of binding assay measuring MHC ligand binding by radioactivity detection using MHC derived from a cell lysate." []
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property_value: IAO:0000231 IAO:0000227
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relationship: IAO:0000231 IAO:0000227
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is_obsolete: true
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replaced_by: OBI:0001544
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```
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For OBO format, there are multiple alternatives:
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1) Use "relationship:" instead of "property_value:".
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1) Use "property_value:" instead of "relationship:".
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1) Use a free text "comment:".
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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:
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```
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[Typedef]

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