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Add workflow to re-wire mappings for obsolete terms

The OMOP2OBO mapping sets contain obsolete/deprecated terms. Add a workflow to the Makefile to update any obsolete term mappings that are in the mappings directory. The general steps should be:

  • Extract the rows with obsolete terms and store them in a separate sssom file.
  • Create a replacement sssom mapping set that maps the obsolete term to the updated term.
    • Retrieve these mappings from CPONT (indicated by oboInOwl:replace_by).
  • Using the replacement mapping set, re-wire the mappings with obsolete terms to use the replacement term.
    • The new mapping justification should be semapv:MappingChaining with both the original mapping set and the replacement set listed as either the mapping_source or mapping_set_source (still need to decide which of these fields should be used for this).