add generation of obsolete triples TTL file and corresponding SPARQL construct query

Author: Robbie1977

dumps.Makefile

@@ -56,7 +56,7 @@ ifndef UNIQUE_FACETS_ANNOTATION
 endif
 
 # The default target that generates all necessary OWL files.
-all: checkenv print_pdb_external_onts print_query_outputs remove_embargoed_data $(FINAL_DUMPS_DIR)/owlery.owl $(FINAL_DUMPS_DIR)/solr.json $(FINAL_DUMPS_DIR)/pdb.owl pdb_csvs pdb_sideloads
+all: checkenv print_pdb_external_onts print_query_outputs remove_embargoed_data $(FINAL_DUMPS_DIR)/owlery.owl $(FINAL_DUMPS_DIR)/solr.json $(FINAL_DUMPS_DIR)/pdb.owl $(FINAL_DUMPS_DIR)/obsolete_triples.ttl pdb_csvs pdb_sideloads
 
 # Declares a phony target to remove embargoed data.
 .PHONY: remove_embargoed_data
@@ -169,6 +169,10 @@ $(FINAL_DUMPS_DIR)/pdb.owl: $(patsubst %, $(RAW_DUMPS_DIR)/construct_%.owl, $(DU
 $(FINAL_DUMPS_DIR)/owlery.owl: $(patsubst %, $(RAW_DUMPS_DIR)/construct_%.owl, $(DUMPS_OWLERY)) $(RAW_DUMPS_DIR)/constructReasoned_merged.owl $(SIDE_LOADING_ONTS)
 	$(call log, $@, $(ROBOT) merge $(patsubst %, -i %, $^) filter --axioms "logical" --preserve-structure true annotate --ontology-iri "http://virtualflybrain.org/data/VFB/OWL/owlery.owl" -o $@ $(STDOUT_FILTER))
 
+# Generates the obsolete triples TTL file for curator review.
+$(FINAL_DUMPS_DIR)/obsolete_triples.ttl: $(RAW_DUMPS_DIR)/obsolete_triples.ttl
+	$(call log, $@, cp $< $@)
+
 # Generates the side loading CSV files for the PDB
 pdb_sideloads: $(SIDE_LOADING_ONTS) | $(CSV_IMPORTS)
 	$(call log, $@, for file in $(SIDE_LOADING_ONTS); do base=$$(basename $$file .owl); var_part=$${base#*_}; java $(ROBOT_ARGS) -jar $(OWL2NEOCSV) $$file "none" $(CSV_IMPORTS) false $(INFER_ANNOTATE_RELATION) $${var_part} only_edges; done)

sparql/construct_obsolete_triples.sparql

@@ -0,0 +1,8 @@
+PREFIX owl: <http://www.w3.org/2002/07/owl#>
+
+CONSTRUCT { ?s ?p ?o . }
+WHERE {
+  ?s ?p ?o .
+  ?o owl:deprecated true .
+  FILTER(?p != owl:deprecated)
+}