This PR amends the rules that refresh the externally maintained SSSOM mapping sets (the sets from FBbt and ZFA) to include a step that check those sets against the current version of the ontology to
(1) remove any mapping to a Uberon entity that does not exist or is deprecated;
(2) add any missing label, using the labels found in the ontology.
This necessitates, as a preliminary:
(1) making sure we are using ODK 1.5.3, as previous versions do not include a recent enough version of SSSOM-Java;
(2) removing a bogus empty xml:base attribute in the XML catalog, that prevents sssom-cli from reading it.
This PR amends the rules that refresh the externally maintained SSSOM mapping sets (the sets from FBbt and ZFA) to include a step that check those sets against the current version of the ontology to
(1) remove any mapping to a Uberon entity that does not exist or is deprecated; (2) add any missing label, using the labels found in the ontology.
This necessitates, as a preliminary:
(1) making sure we are using ODK 1.5.3, as previous versions do not include a recent enough version of SSSOM-Java; (2) removing a bogus empty xml:base attribute in the XML catalog, that prevents sssom-cli from reading it.