I have a database storing genotype data. I also want to add phenotype data by using terms taken from the Human Phenotype Ontology.
When the phenotype ontology is updated, if a term I have used becomes obsolete, I will need to replace the obsolete term with a newer equivalent. I notice OBO defines tags "replaced_by" which indicates an alternative term that can be used to automatically replace the obsoleted term and "consider" which is similar but needs additional human intervention. Unfortunately the ontology I am interested in using does not seem to provide these attributes.
Apart from the two obvious ways to manage this i.e "use one version of the ontology and never update" or "just prompt the user to redo the annotation for expired terms", is there another established way to automatically identify replacements for obsoleted terms in an ontology? For example it seems as though some information from the relationships in the two ontology graphs could be exploited here?
If anyone could suggest a paper dealing with this problem I would be very grateful.