node identifiers

Makefile

@@ -22,8 +22,11 @@ STAGED_ONTOLOGIES = $(patsubst %, stage/%.db.gz, $(ALL_ONTS))
 TEST_ONTOLOGIES = go-nucleus robot-example
 
 
+include ontologies.Makefile
+
 all: build_all stage_all
-build_all: $(patsubst %,all-%,$(ALL_ONTS))
+build_all: $(patsubst %, all-%, $(ALL_ONTS))
+	echo building $(ALL_ONTS)
 stage_all: $(STAGED_ONTOLOGIES)
 	echo done $(STAGED_ONTOLOGIES)
 
@@ -79,17 +82,17 @@ realclean-%:
 
 build_prefixes: $(PREFIX_DIR)/prefixes.csv
 
-$(PREFIX_DIR)/obo_prefixes.owl:
-	robot convert -I http://purl.obolibrary.org/meta/obo_prefixes.ttl -o $@
+#$(PREFIX_DIR)/obo_prefixes.owl:
+#	robot convert -I http://purl.obolibrary.org/meta/obo_prefixes.ttl -o $@
 
-$(PREFIX_DIR)/obo_prefixes.db: $(PREFIX_DIR)/obo_prefixes.owl
-	sqlite3 $@ < $(PREFIX_DIR)/prefix_ddl.sql && ./bin/rdftab $@ < $<
+#$(PREFIX_DIR)/obo_prefixes.db: $(PREFIX_DIR)/obo_prefixes.owl
+#	sqlite3 $@ < $(PREFIX_DIR)/prefix_ddl.sql && ./bin/rdftab $@ < $<
 
-$(PREFIX_DIR)/obo_prefixes.csv: $(PREFIX_DIR)/obo_prefixes.db
-	sqlite3 $< -cmd ".separator ','" "SELECT p.value AS prefix, ns.value AS base FROM statements AS p JOIN statements AS ns ON (p.subject=ns.subject) WHERE p.predicate='<http://www.w3.org/ns/shacl#prefix>' AND ns.predicate='<http://www.w3.org/ns/shacl#namespace>'" > $@
+#$(PREFIX_DIR)/obo_prefixes.csv: $(PREFIX_DIR)/obo_prefixes.db
+#	sqlite3 $< -cmd ".separator ','" "SELECT p.value AS prefix, ns.value AS base FROM statements AS p JOIN statements AS ns ON (p.subject=ns.subject) WHERE p.predicate='<http://www.w3.org/ns/shacl#prefix>' AND ns.predicate='<http://www.w3.org/ns/shacl#namespace>'" > $@
 
-$(PREFIX_DIR)/prefixes.csv: $(PREFIX_DIR)/prefixes_curated.csv $(PREFIX_DIR)/obo_prefixes.csv
-	cat $^ > $@
+#$(PREFIX_DIR)/prefixes.csv: $(PREFIX_DIR)/prefixes_curated.csv $(PREFIX_DIR)/obo_prefixes.csv#
+#	cat $^ > $@
 
 
 # ---
@@ -133,13 +136,6 @@ reports/%.problems.tsv: db/%.db target/%.views
 STAMP:
 	touch $@
 
-db/reactome-Homo-sapiens.owl: download/reactome-biopax.zip db/biopax.owl
-	unzip -p $< Homo_sapiens.owl > $@.tmp &&\
-	robot merge -i $@.tmp  -i db/biopax.owl -o $@
-
-download/reactome-biopax.zip:
-	curl -L -s https://reactome.org/download/current/biopax.zip > $@
-
 ## Additional ontologies
 
 src/semsql/builder/registry/registry_schema.py: src/semsql/builder/registry/registry_schema.yaml

ontologies.Makefile

@@ -28,7 +28,7 @@ download/maxo.owl: STAMP
 .PRECIOUS: download/maxo.owl
 
 db/maxo.owl: download/maxo.owl
-	robot relax -i $< merge -o $@
+	robot relax -i $< merge reason -r structural -o $@
 
 
 download/foodon.owl: STAMP
@@ -372,6 +372,50 @@ db/uniprot.owl: download/uniprot.owl
 	cp $< $@
 
 
+download/rhea.owl: STAMP
+	curl -L -s https://github.com/biopragmatics/obo-db-ingest/raw/main/export/rhea/122/rhea.owl.gz | gzip -dc > $@.tmp
+	sha256sum -b $@.tmp > $@.sha256
+	mv $@.tmp $@
+
+.PRECIOUS: download/rhea.owl
+
+db/rhea.owl: download/rhea.owl
+	cp $< $@
+
+
+download/drugbank.owl: STAMP
+	curl -L -s https://github.com/biopragmatics/obo-db-ingest/raw/main/export/drugbank/5.1.9/drugbank.owl.gz | gzip -dc > $@.tmp
+	sha256sum -b $@.tmp > $@.sha256
+	mv $@.tmp $@
+
+.PRECIOUS: download/drugbank.owl
+
+db/drugbank.owl: download/drugbank.owl
+	cp $< $@
+
+
+download/drugcentral.owl: STAMP
+	curl -L -s https://github.com/biopragmatics/obo-db-ingest/raw/main/export/drugcentral.owl.gz | gzip -dc > $@.tmp
+	sha256sum -b $@.tmp > $@.sha256
+	mv $@.tmp $@
+
+.PRECIOUS: download/drugcentral.owl
+
+db/drugcentral.owl: download/drugcentral.owl
+	cp $< $@
+
+
+download/complexportal.owl: STAMP
+	curl -L -s https://github.com/biopragmatics/obo-db-ingest/raw/main/export/complexportal/2022-02-03/complexportal.owl.gz | gzip -dc > $@.tmp
+	sha256sum -b $@.tmp > $@.sha256
+	mv $@.tmp $@
+
+.PRECIOUS: download/complexportal.owl
+
+db/complexportal.owl: download/complexportal.owl
+	cp $< $@
+
+
 download/%.owl: STAMP
 	curl -L -s http://purl.obolibrary.org/obo/$*.owl > $@.tmp
 	sha256sum -b $@.tmp > $@.sha256
@@ -382,4 +426,4 @@ download/%.owl: STAMP
 db/%.owl: download/%.owl
 	robot merge -i $< -o $@
 
-EXTRA_ONTOLOGIES = chiro ncit maxo foodon chebiplus msio phenio comploinc bero aio reacto go go-lego bao orcid cpont biolink biopax enanomapper mlo ito reactome-Homo-sapiens efo edam sweetAll lov schema-dot-org cosmo co_324 hgnc.genegroup hgnc dictybase eccode uniprot
+EXTRA_ONTOLOGIES = chiro ncit maxo foodon chebiplus msio phenio comploinc bero aio reacto go go-lego bao orcid cpont biolink biopax enanomapper mlo ito reactome-Homo-sapiens efo edam sweetAll lov schema-dot-org cosmo co_324 hgnc.genegroup hgnc dictybase eccode uniprot rhea drugbank drugcentral complexportal

src/semsql/builder/build.Makefile

@@ -95,7 +95,7 @@ $(PREFIX_DIR)/obo_prefixes.owl:
 	robot convert -I http://purl.obolibrary.org/meta/obo_prefixes.ttl -o $@
 
 $(PREFIX_DIR)/obo_prefixes.db: $(PREFIX_DIR)/obo_prefixes.owl
-	sqlite3 $@ < $(PREFIX_DIR)/prefix_ddl.sql && ./bin/rdftab $@ < $<
+	sqlite3 $@ < $(PREFIX_DIR)/prefix_ddl.sql && rdftab $@ < $<
 
 $(PREFIX_DIR)/obo_prefixes.csv: $(PREFIX_DIR)/obo_prefixes.db
 	sqlite3 $< -cmd ".separator ','" "SELECT p.value AS prefix, ns.value AS base FROM statements AS p JOIN statements AS ns ON (p.subject=ns.subject) WHERE p.predicate='<http://www.w3.org/ns/shacl#prefix>' AND ns.predicate='<http://www.w3.org/ns/shacl#namespace>'" > $@