Refresh ENVO imports and cleans them (#1529)

* Uncomment the import generation process and prune CL/CARO ID spaces

For some reason the import generation process was frozen, unfreezing.

Also we prune out CARO and CL references as we do not import them in ENVO.

* Add PATO_0001739 declaration to patch missing term in seed

An axiom in some envo bridge needed this PATO term, but the import process does not import it. For patchwork, this is adding a declaration to the edit file.

* Refresh all envo imports

src/envo/Makefile

@@ -338,8 +338,8 @@ imports/%_combined_seed.tsv: imports/%_terms.txt imports/seed.txt
 # We use the standard catalog, but rewrite the import to X to be a local mirror of ALL of X.
 # After extraction, we further reduce the ontology by creating a "mingraph" (removes all annotations except label) and by
 imports/%_import.owl: mirror/%.owl envo-edit.owl imports/%_combined_seed.tsv
-	echo "Skipping"
-	#$(ROBOT) extract -i $< -T imports/$*_combined_seed.tsv -m BOT -O $(ENVO_IMPORTS_BASE_URI)/$@ -o [email protected] && mv [email protected] $@
+	$(ROBOT) extract -i $< -T imports/$*_combined_seed.tsv -m BOT -O $(ENVO_IMPORTS_BASE_URI)/$@ \
+		remove --select "<http://purl.obolibrary.org/obo/CL_*>" remove --select "<http://purl.obolibrary.org/obo/CARO_*>"  -o $@.tmp.owl && mv $@.tmp.owl $@
 
 imports/%_import.obo: imports/%_import.owl
 	$(OWLTOOLS) $(USECAT) $< -o -f obo --no-check $@

src/envo/envo-edit.owl

@@ -4228,6 +4228,7 @@ Declaration(Class(<http://purl.obolibrary.org/obo/PATO_0001360>))
 Declaration(Class(<http://purl.obolibrary.org/obo/PATO_0001576>))
 Declaration(Class(<http://purl.obolibrary.org/obo/PATO_0001595>))
 Declaration(Class(<http://purl.obolibrary.org/obo/PATO_0001657>))
+Declaration(Class(<http://purl.obolibrary.org/obo/PATO_0001739>))
 Declaration(Class(<http://purl.obolibrary.org/obo/PATO_0001759>))
 Declaration(Class(<http://purl.obolibrary.org/obo/PATO_0001997>))
 Declaration(Class(<http://purl.obolibrary.org/obo/PATO_0040008>))