Adding reason step for maxo

Author: cmungall

Makefile

@@ -17,21 +17,24 @@ SELECTED_ONTS = obi mondo go envo ro hp mp zfa wbphenotype ecto upheno uberon_cm
 # EXTRA_ONTOLOGIES is defined in ontologies.Makefile
 ALL_ONTS = $(ALL_OBO_ONTS) $(EXTRA_ONTOLOGIES)
 
-STAGED_ONTOLOGIES = $(patsubst %,stage/%.db.gz,$(ALL_ONTS))
+STAGED_ONTOLOGIES = $(patsubst %, stage/%.db.gz, $(ALL_ONTS))
 
 TEST_ONTOLOGIES = go-nucleus robot-example
 
 
 all: build_all stage_all
 build_all: $(patsubst %,all-%,$(ALL_ONTS))
 stage_all: $(STAGED_ONTOLOGIES)
+	echo done $(STAGED_ONTOLOGIES)
 
 selected: $(patsubst %,all-%,$(SELECTED_ONTS))
 
 all-%: db/%.db
 	sqlite3 $< "SELECT COUNT(*) FROM statements"
-stage/%.db.gz: db/%.db
-	gzip -c $< > $@.tmp && mv $@.tmp $@
+#stage/%.db.gz: db/%.db
+#	gzip -c $< > [email protected] && mv [email protected] $@
+stage/%.db.gz: 
+	gzip -c db/$*.db > $@.tmp && mv $@.tmp $@
 .PRECIOUS: stage/%.db.gz
 
 list-onts:

ontologies.Makefile

@@ -20,6 +20,17 @@ db/ncit.owl: download/ncit.owl
 	robot relax -i $< merge -o $@
 
 
+download/maxo.owl: STAMP
+	curl -L -s http://purl.obolibrary.org/obo/maxo.owl > $@.tmp
+	sha256sum -b $@.tmp > $@.sha256
+	mv $@.tmp $@
+
+.PRECIOUS: download/maxo.owl
+
+db/maxo.owl: download/maxo.owl
+	robot relax -i $< merge -o $@
+
+
 download/foodon.owl: STAMP
 	curl -L -s http://purl.obolibrary.org/obo/foodon.owl > $@.tmp
 	sha256sum -b $@.tmp > $@.sha256
@@ -371,4 +382,4 @@ download/%.owl: STAMP
 db/%.owl: download/%.owl
 	robot merge -i $< -o $@
 
-EXTRA_ONTOLOGIES = chiro ncit 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

src/semsql/builder/registry/ontologies.yaml

@@ -8,6 +8,10 @@ ontologies:
   ncit:
     url: http://purl.obolibrary.org/obo/ncit.owl
     build_command: "robot relax -i $< merge -o $@"
+  maxo:
+    url: http://purl.obolibrary.org/obo/maxo.owl
+    # https://github.com/monarch-initiative/MAxO/issues/367
+    build_command: "robot relax -i $< merge reason -r structural -o $@"
   foodon:
     url: http://purl.obolibrary.org/obo/foodon.owl
     build_command: "robot merge -i $< relax reduce -c true -o $@"