Update GARD mappings (major) (#6347)

* Update mondo.Makefile

* Update mondo-edit.obo

* Update mondo.Makefile

* Update mondo.Makefile

* Update mondo-edit.obo

* - Bugfix: deprecated_annotation_merging: Now correctly replaces/reorders these annotations.

* Update mondo-edit.obo

* Update gard

* Mondo::GARD obsoletes (#6451)

* Mondo::GARD obsoletes
- Getting a list of all Mondo terms that are obsoleted and have a GARD relationship.

* Mondo::GARD obsoletes
- Update: Changed implementation from OAK to SPARQL. The only reason for this is in order to get obsolete reason.

* Mondo::GARD obsoletes
- Update: Made rdfs:comment optional
- Added: Obsolescence reason 'IAO_0000231'

* Update mondo.Makefile

* Remove old GARD mappings from Mondo

* Update obsolete list

---------

Co-authored-by: joeflack4 <[email protected]>

.gitignore

@@ -52,7 +52,8 @@ src/ontology/mondo.json
 src/ontology/mondo.obo
 src/ontology/mondo.owl
 src/ontology/reasoned.owl
-src/ontology/reports
+src/ontology/reports/*
+!src/ontology/reports/gard-mondo-mapped-obsoletes.tsv
 src/ontology/test_nomerge
 src/ontology/subsets/mondo-minimal.owl.tmp2.owl
 src/ontology/subsets/mondo-minimal.owl.tmp.owl

src/ontology/Makefile

@@ -271,9 +271,9 @@ $(ONT)-with-equivalents.json: $(ONT)-with-equivalents.owl
 # we remove imports and merge in additional assertions
 # note: typically component is not pre-reasoned, but this is compex for mondo.
 
-OTHER_SRC=imports/axioms.owl components/mondo-subsets.owl
+OTHER_SRC=imports/axioms.owl components/mondo-subsets.owl #components/mondo-tags.owl
 
-$(ONT)-base.owl: reasoned.owl
+$(ONT)-base.owl: reasoned.owl $(OTHER_SRC)
 	$(ROBOT) remove --input $< --select imports --trim false \
 		merge $(patsubst %, -i %, $(OTHER_SRC)) \
 		annotate --annotation http://purl.org/dc/elements/1.1/type http://purl.obolibrary.org/obo/IAO_8000001 \
@@ -371,7 +371,8 @@ subsets/%.obo: subsets/%.owl
 	$(ROBOT) convert -i $< -o $@.tmp.obo && grep -v ^owl-axioms: $@.tmp.obo > $@ && rm $@.tmp.obo
 
 rare_subset:
-	$(MAKE) IMP=false MIR=false COMP=false subsets/mondo-rare.owl
+	$(MAKE) IMP=false MIR=false COMP=false components/mondo-subsets.owl
+	$(MAKE) IMP=false MIR=false COMP=false subsets/mondo-rare.owl subsets/mondo-rare.json subsets/mondo-rare.obo
 
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