Fix generation of prefixes yaml for custom prefix maps

Makefile

@@ -220,6 +220,9 @@ s3-deploy:
 	aws s3 sync stage s3://bbop-sqlite --acl public-read && \
 	aws s3 sync stage s3://bbop-sqlite/releases/$(DATE) --acl public-read
 
+s3-deploy-%: stage/%.db.gz
+	aws s3 cp $< s3://bbop-sqlite/$*.db.gz --acl public-read
+
 ################################################
 #### Commands for building the Docker image ####
 ################################################

src/semsql/builder/build.Makefile

@@ -64,16 +64,19 @@ PREFIX_YAML_PATH = $(PREFIX_DIR)/prefixes.yaml
 	mv $@.tmp $@
 .PRECIOUS: %.db
 
+%-prefixes.yaml: $(PREFIX_CSV_PATH)
+	grep -v ^prefix, $< | grep -v ^obo, | perl -npe 's@,(.*)@: "$$1"@'  > $@.tmp && mv $@.tmp $@
+
 # -- ENTAILED EDGES --
 # relation-graph is used to compute entailed edges.
-%-$(RGSUFFIX).tsv: %-min.owl %-properties.txt $(PREFIX_YAML_PATH)
+%-$(RGSUFFIX).tsv: %-min.owl %-properties.txt %-prefixes.yaml
 	$(RG) --disable-owl-nothing true \
                        --ontology-file $<\
 		       $(RG_PROPERTIES) \
                        --output-file $@.tmp \
                        --equivalence-as-subclass true \
                        --mode TSV \
-		       --prefixes $(PREFIX_YAML_PATH) \
+		       --prefixes $*-prefixes.yaml \
 	               --output-individuals true \
 	               --output-subclasses true \
                        --reflexive-subclasses true && \

src/semsql/linkml/relation_graph.yaml

@@ -53,6 +53,9 @@ classes:
         SELECT subject, predicate, object
         FROM rdfs_subclass_of_named_statement
          UNION
+        SELECT subject, predicate, object
+         FROM rdfs_subproperty_of_statement
+         UNION
         SELECT subject, predicate, object
         FROM rdf_type_statement WHERE object IN (SELECT id FROM class_node)
     in_subset: