odk.yaml bdscratch to bdso rename

Author: hkir-dev

src/ontology/Makefile

@@ -1,9 +1,9 @@
 # ----------------------------------------
-# Makefile for bdscratch
+# Makefile for bdso
 # Generated using ontology-development-kit
 # ODK Version: v1.2.32
 # ----------------------------------------
-# IMPORTANT: DO NOT EDIT THIS FILE. To override default make goals, use bdscratch.Makefile instead
+# IMPORTANT: DO NOT EDIT THIS FILE. To override default make goals, use bdso.Makefile instead
 
 
 # ----------------------------------------
@@ -228,7 +228,7 @@ imports/%_terms_combined.txt: $(IMPORTSEED) imports/%_terms.txt
 
 
 imports/merged_import.owl: mirror/merged.owl imports/merged_terms_combined.txt
-	echo "ERROR: You have configured your default module type to be slme; this behavior needs to be overwritten in bdscratch.Makefile!" && false
+	echo "ERROR: You have configured your default module type to be slme; this behavior needs to be overwritten in bdso.Makefile!" && false
 
 
 
@@ -527,7 +527,7 @@ SHARED_ROBOT_COMMANDS =
 
 $(ONTOLOGYTERMS): $(SRC) $(OTHER_SRC)
 	touch $(ONTOLOGYTERMS) && \
-	$(ROBOT) query --use-graphs true -f csv -i $< --query ../sparql/bdscratch_terms.sparql $@
+	$(ROBOT) query --use-graphs true -f csv -i $< --query ../sparql/bdso_terms.sparql $@
 
 
 
@@ -597,12 +597,12 @@ normalize_src: $(SRC)
 
 .PHONY: validate_idranges
 validate_idranges:
-	amm $(SCRIPTSDIR)/validate_id_ranges.sc bdscratch-idranges.owl
+	amm $(SCRIPTSDIR)/validate_id_ranges.sc bdso-idranges.owl
 
 .PHONY: update_repo
 update_repo:
 	sh $(SCRIPTSDIR)/update_repo.sh
 
 
 
-include bdscratch.Makefile
+include bdso.Makefile

src/ontology/bdscratch-odk.yaml renamed to src/ontology/bdso-odk.yaml

@@ -1,7 +1,7 @@
-id: bdscratch
+id: bdso
 title: Brain Data Standards Cell Ontology
 github_org: obophenotype
-repo: bdscratch
+repo: bdso
 use_dosdps: TRUE
 export_formats:
   - owl

src/ontology/bdscratch.Makefile renamed to src/ontology/bdso.Makefile

@@ -4,7 +4,7 @@ echo "(2) and add missing files, if any."
 
 set -e
 
-OID=bdscratch
+OID=bdso
 ROOTDIR=../..
 SRCDIR=..
 CONFIG=$OID"-odk.yaml"

src/scripts/update_repo.sh

@@ -5,7 +5,7 @@ query language for RDF. This directory contains useful SPARQL queries
 for perfoming over the ontology.
 
 SPARQL can be executed on a triplestore or directly on any OWL
-file. The queries here are all executed on either bdscratch-edit.obo or
+file. The queries here are all executed on either bdso-edit.obo or
 downstream products in the [ontology](../ontology/) folder. We use
 `robot` as this allows easy execution over any Obo-format or OWL file.
 

src/sparql/README.md

@@ -0,0 +1,7 @@
+SELECT DISTINCT ?term
+WHERE {
+  { ?s1 ?p1 ?term . }
+  UNION
+  { ?term ?p2 ?o2 . }
+  FILTER(isIRI(?term) && (regex(str(?term), UCASE("bdso_"))))
+}