We need to change ontology so that mere synonyms are listed not as separated properties, but as (I would suggest) obo:hasExactSynonym annotations of canonical relations. The obo synonym annotation properties are also used by EDAM. We also need to attach the papers_with_code_id property of those relations to the canonical property instead.
SUGGESTION: Since this would be tedious to do fully manually, I suggest you simply mark all the 'synonym' metrics with refactor_comment 'synonym'. I can then write code so that the marked properties are automatically merged into their superproperties!
We need to change ontology so that mere synonyms are listed not as separated properties, but as (I would suggest) obo:hasExactSynonym annotations of canonical relations. The obo synonym annotation properties are also used by EDAM. We also need to attach the papers_with_code_id property of those relations to the canonical property instead.
SUGGESTION: Since this would be tedious to do fully manually, I suggest you simply mark all the 'synonym' metrics with refactor_comment 'synonym'. I can then write code so that the marked properties are automatically merged into their superproperties!