Update make pipeline

obophenotype · Nov 23, 2021 · 61aac21 · 61aac21
1 parent 5b162e0
commit 61aac21
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Showing 3 changed files with 28 additions and 2 deletions.
diff --git a/src/ontology/cl.Makefile b/src/ontology/cl.Makefile
@@ -68,12 +68,13 @@ tmp/asserted-subclass-of-axioms.obo: $(SRC) tmp/cl_terms.txt
 # into existentials on roundtrip
 
 tmp/source-merged.obo: $(SRC) tmp/asserted-subclass-of-axioms.obo config/remove_annotations.txt
-	$(ROBOT) merge --input $< \
+	$(ROBOT) merge --input $(SRC) \
 		reason --reasoner ELK \
 		relax \
 		remove --axioms equivalent \
 		merge -i tmp/asserted-subclass-of-axioms.obo \
 		remove -T config/remove_annotations.txt --axioms annotation \
+		query --update ../sparql/remove-op-definitions.ru \
 		convert --check false -f obo $(OBO_FORMAT_OPTIONS) -o tmp/source-merged.owl.obo &&\
 		grep -v ^owl-axioms tmp/source-merged.owl.obo > tmp/source-stripped2.obo &&\
 		grep -v '^def[:][ ]["]x[ ]only[ ]in[ ]taxon' tmp/source-stripped2.obo > tmp/source-stripped3.obo &&\

diff --git a/src/ontology/config/remove_annotations.txt b/src/ontology/config/remove_annotations.txt
@@ -8,4 +8,5 @@ RO:0002220
 BSPO:0000126
 BFO:0000062
 RO:0002161
-BSPO:0001108
+BSPO:0001108
+RO:0002373
diff --git a/src/sparql/remove-op-definitions.ru b/src/sparql/remove-op-definitions.ru
@@ -0,0 +1,24 @@
+PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
+PREFIX description: <http://purl.obolibrary.org/obo/IAO_0000115>
+PREFIX owl: <http://www.w3.org/2002/07/owl#>
+
+
+DELETE {
+  ?sub description: ?obj .
+  ?relax a owl:Axiom ;
+         owl:annotatedSource ?sub ;
+         owl:annotatedProperty description: ;
+         owl:annotatedTarget ?obj ;
+         ?a ?b .
+}
+WHERE {
+  {
+    ?sub description: ?obj .
+    ?relax a owl:Axiom ;
+           owl:annotatedSource ?sub ;
+           owl:annotatedProperty description: ;
+           owl:annotatedTarget ?obj ;
+           ?a ?b .
+    FILTER (ISIRI(?sub) && STRSTARTS(STR(?sub), "http://purl.obolibrary.org/obo/RO_"))
+  }
+}