new release

oborel · Aug 25, 2016 · fc42248 · fc42248
1 parent 4afcf47
commit fc42248
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Showing 36 changed files with 4,836 additions and 2,012 deletions.
diff --git a/ro.obo b/ro.obo
diff --git a/ro.owl b/ro.owl
diff --git a/src/ontology/Makefile b/src/ontology/Makefile
@@ -18,6 +18,10 @@ ro.owl: ro-edit.owl core.owl temporal-intervals.owl validate-using-oort
 	owltools $<  --set-ontology-id -v $(OBO)/ro/releases/`date +%Y-%m-%d`/ro.owl $(OBO)/ro.owl -o file://`pwd`/$@
 #	grep versionIRI $< && (echo "check the version:" && echo versionIRI: `grep versionIRI $<` && cp $< $@) || echo 'You must set the versionIRI!!'
 
+# turtle file is merged, for querying via arq
+ro.ttl: ro.owl
+	owltools --use-catalog $< --merge-import-closure -o -f ttl $@.tmp && mv $@.tmp $@
+
 %.obo: %.owl
 	owltools --use-catalog $< --merge-import-closure -o -f obo $@.tmp && grep -v ^synonym $@.tmp > $@
 #	obolib-owl2obo -o [email protected] $< && grep -v ^import: [email protected] > $@
@@ -125,6 +129,19 @@ odp/%.owl:
 	wget http://www.ontologydesignpatterns.org/cp/owl/$*.owl -O $@
 
 
+# ----------------------------------------
+# Reports
+# ----------------------------------------
+REPORTS=basicReport
+all_reports: $(patsubst %, reports/envo-%.csv, $(REPORTS))
+
+reports/ro-%.csv: ro.ttl sparql/%.sparql
+	arq --data $< --query sparql/$*.sparql --results csv > $@.tmp && mv $@.tmp $@
+
+reports/ro-%.ttl: ro.ttl sparql/%.sparql
+	arq --data $< --query sparql/$*.sparql --results ttl > $@.tmp && mv $@.tmp $@
+
+
 # ----------------------------------------
 # MARKDOWN EXPORT
 # ----------------------------------------

diff --git a/src/ontology/reports/ro-objectProperties.csv b/src/ontology/reports/ro-objectProperties.csv
diff --git a/src/ontology/ro-edit.owl b/src/ontology/ro-edit.owl
diff --git a/src/ontology/ro.obo b/src/ontology/ro.obo
diff --git a/src/ontology/ro.owl b/src/ontology/ro.owl
diff --git a/src/ontology/subsets/ro-causal.obo b/src/ontology/subsets/ro-causal.obo
diff --git a/src/ontology/subsets/ro-causal.owl b/src/ontology/subsets/ro-causal.owl
diff --git a/src/ontology/subsets/ro-developmental.obo b/src/ontology/subsets/ro-developmental.obo
diff --git a/src/ontology/subsets/ro-developmental.owl b/src/ontology/subsets/ro-developmental.owl
diff --git a/src/ontology/subsets/ro-eco.obo b/src/ontology/subsets/ro-eco.obo
diff --git a/src/ontology/subsets/ro-eco.owl b/src/ontology/subsets/ro-eco.owl
diff --git a/src/ontology/subsets/ro-interaction.obo b/src/ontology/subsets/ro-interaction.obo
diff --git a/src/ontology/subsets/ro-interaction.owl b/src/ontology/subsets/ro-interaction.owl
diff --git a/src/ontology/subsets/ro-mereotopology.obo b/src/ontology/subsets/ro-mereotopology.obo
diff --git a/src/ontology/subsets/ro-mereotopology.owl b/src/ontology/subsets/ro-mereotopology.owl
diff --git a/src/ontology/subsets/ro-sequence.obo b/src/ontology/subsets/ro-sequence.obo
diff --git a/src/ontology/subsets/ro-sequence.owl b/src/ontology/subsets/ro-sequence.owl
diff --git a/src/ontology/subsets/ro-time-interval.obo b/src/ontology/subsets/ro-time-interval.obo
diff --git a/src/ontology/subsets/ro-time-interval.owl b/src/ontology/subsets/ro-time-interval.owl
diff --git a/subsets/ro-causal.obo b/subsets/ro-causal.obo
diff --git a/subsets/ro-causal.owl b/subsets/ro-causal.owl
diff --git a/subsets/ro-chado.obo b/subsets/ro-chado.obo
@@ -9,7 +9,7 @@ remark: Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo
 remark: Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/ro/pato_import.owl>))) [Axioms: 20 Logical Axioms: 6]
 remark: Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/ro/rohom.owl>))) [Axioms: 731 Logical Axioms: 148]
 remark: Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/ro/temporal-intervals.owl>))) [Axioms: 146 Logical Axioms: 45]
-default-namespace: relationship
+default-namespace: ro
 ontology: ro/subsets/ro-chado.obo
 property_value: http://purl.org/dc/elements/1.1/description "The OBO Relations Ontology (RO) is a collection of OWL relations (ObjectProperties) intended for use across a wide variety of biological ontologies." xsd:string
 property_value: http://purl.org/dc/elements/1.1/source http://obofoundry.org/ro
@@ -3032,3 +3032,8 @@ def: "The relationship that links an entity with the process that results in the
 is_a: results_in_developmental_progression_of ! results in developmental progression of
 is_a: RO:0000057 ! has participant
 
+[Typedef]
+id: OBO_REL:is_a
+name: is_a
+comment: This relation is added for backward compatibility with Chado
+
diff --git a/subsets/ro-developmental.obo b/subsets/ro-developmental.obo
diff --git a/subsets/ro-developmental.owl b/subsets/ro-developmental.owl
diff --git a/subsets/ro-eco.obo b/subsets/ro-eco.obo
diff --git a/subsets/ro-eco.owl b/subsets/ro-eco.owl
diff --git a/subsets/ro-interaction.obo b/subsets/ro-interaction.obo
diff --git a/subsets/ro-interaction.owl b/subsets/ro-interaction.owl
diff --git a/subsets/ro-mereotopology.obo b/subsets/ro-mereotopology.obo
diff --git a/subsets/ro-mereotopology.owl b/subsets/ro-mereotopology.owl
diff --git a/subsets/ro-sequence.obo b/subsets/ro-sequence.obo
diff --git a/subsets/ro-sequence.owl b/subsets/ro-sequence.owl
diff --git a/subsets/ro-time-interval.obo b/subsets/ro-time-interval.obo
diff --git a/subsets/ro-time-interval.owl b/subsets/ro-time-interval.owl