how to relate a deprecated term due to merge or replace

[zhengj2007]

Some use annotationProperty:has_alternative_id (OBO), to associate the term with deprecated term (using ID), for example, http://purl.obolibrary.org/obo/PATO_0001018, http://purl.obolibrary.org/obo/PATO_0001241

Some use annotationProperty:term replaced by (IAO), to associated the deprecated term with the term (using IRI) that replaced it, for example, http://purl.obolibrary.org/obo/OBI_1110055

Shall we use both annotationProperties? So we can find deprecated term/replaced terms in both directions. Should we use ontology term ID or IRI for reference?

[cmungall]

has_alternative_id is deprecated. Note the reciprocal info is available from the deprecated term: http://purl.obolibrary.org/obo/PATO_0002079 (uses IAO replaced by)

For history, see: owlcs/owlapi#317

[cmungall]

A is merged into B

Class: A
Annotations: 
  is_deprecated="true"^^xsd:boolean
  IAO:0000231=IAO:0000225
  IAO:0100001=B

A is obsoleted and replaced by B

Class: A
Annotations: 
  rdfs:label="obsolete foo"
  <other annotation assertions>
  is_deprecated="true"^^xsd:boolean
  IAO:0100001=B

A is obsoleted and there is no direct replacement

for scenario when A is obsoleted, and B and C are potential replacements to be evaluated manually

Class: A
Annotations: 
  rdfs:label="obsolete foo"
  <other annotation assertions>
  is_deprecated="true"^^xsd:boolean
  oboInOwl:consider=B
  oboInOwl:consider=C

cardinality of consider is 0..*

[zhengj2007]

Discussed on 2018-12-4 OFOC call.

has_alternative_id is deprecated in PATO. The deprecation annotation properties are used consistently in OBO ontologies now.