remove cob import

src/ontology/Makefile

@@ -109,7 +109,7 @@ all_main: $(MAIN_FILES)
 # ----------------------------------------
 
 
-IMPORTS =  omo pato cl envo go other orcidio uberon cob obi
+IMPORTS =  omo pato cl envo go other orcidio uberon obi
 
 IMPORT_ROOTS = $(patsubst %, $(IMPORTDIR)/%_import, $(IMPORTS))
 IMPORT_OWL_FILES = $(foreach n,$(IMPORT_ROOTS), $(n).owl)
@@ -378,16 +378,6 @@ $(IMPORTDIR)/uberon_import.owl: $(MIRRORDIR)/uberon.owl $(IMPORTDIR)/uberon_term
 		query --update ../sparql/inject-subset-declaration.ru --update ../sparql/inject-synonymtype-declaration.ru --update ../sparql/postprocess-module.ru \
 		$(ANNOTATE_CONVERT_FILE); fi
 
-## Module for ontology: cob
-
-$(IMPORTDIR)/cob_import.owl: $(MIRRORDIR)/cob.owl $(IMPORTDIR)/cob_terms_combined.txt
-	if [ $(IMP) = true ]; then $(ROBOT) query -i $< --update ../sparql/preprocess-module.ru \
-    extract -T $(IMPORTDIR)/cob_terms_combined.txt --copy-ontology-annotations true --force true --method BOT \
-    remove --base-iri $(OBOBASE)/COB --axioms external --preserve-structure false --trim false \
-		remove $(patsubst %, --term %, $(ANNOTATION_PROPERTIES)) -T $(IMPORTDIR)/cob_terms_combined.txt --select complement \
-		query --update ../sparql/inject-subset-declaration.ru --update ../sparql/inject-synonymtype-declaration.ru --update ../sparql/postprocess-module.ru \
-		$(ANNOTATE_CONVERT_FILE); fi
-
 ## Module for ontology: obi
 
 $(IMPORTDIR)/obi_import.owl: $(MIRRORDIR)/obi.owl $(IMPORTDIR)/obi_terms_combined.txt
@@ -537,15 +527,6 @@ mirror-uberon: | $(TMPDIR)
 		mv $@.tmp.owl $(TMPDIR)/$@.owl; fi
 
 
-## ONTOLOGY: cob
-.PHONY: mirror-cob
-.PRECIOUS: $(MIRRORDIR)/cob.owl
-mirror-cob: | $(TMPDIR)
-	if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/cob.owl --create-dirs -o $(MIRRORDIR)/cob.owl --retry 4 --max-time 200 &&\
-		$(ROBOT) convert -i $(MIRRORDIR)/cob.owl -o $@.tmp.owl &&\
-		mv $@.tmp.owl $(TMPDIR)/$@.owl; fi
-
-
 ## ONTOLOGY: obi
 .PHONY: mirror-obi
 .PRECIOUS: $(MIRRORDIR)/obi.owl

src/ontology/catalog-v001.xml

@@ -1,7 +1,6 @@
 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
 <catalog prefer="public" xmlns="urn:oasis:names:tc:entity:xmlns:xml:catalog">
     <group id="Folder Repository, directory=, recursive=false, Auto-Update=false, version=2" prefer="public" xml:base="">
-        <uri name="http://purl.obolibrary.org/obo/ro/imports/cob_import.owl" uri="imports/cob_import.owl"/>
         <uri name="http://purl.obolibrary.org/obo/ro/imports/uberon_import.owl" uri="imports/uberon_import.owl"/>
         <uri name="http://purl.obolibrary.org/obo/ro/imports/obi_import.owl" uri="imports/obi_import.owl"/>
         <uri name="http://purl.obolibrary.org/obo/ro/imports/omo_import.owl" uri="imports/omo_import.owl"/>

src/ontology/ro-edit.owl

@@ -32,7 +32,6 @@ Import(<http://purl.obolibrary.org/obo/ro/imports/omo_import.owl>)
 Import(<http://purl.obolibrary.org/obo/ro/imports/orcidio_import.owl>)
 Import(<http://purl.obolibrary.org/obo/ro/imports/other_import.owl>)
 Import(<http://purl.obolibrary.org/obo/ro/imports/pato_import.owl>)
-Import(<http://purl.obolibrary.org/obo/ro/imports/cob_import.owl>)
 Import(<http://purl.obolibrary.org/obo/ro/imports/obi_import.owl>)
 Import(<http://purl.obolibrary.org/obo/ro/imports/uberon_import.owl>)
 Annotation(dc:description "The OBO Relations Ontology (RO) is a collection of OWL relations (ObjectProperties) intended for use across a wide variety of biological ontologies."@en)

src/ontology/ro-odk.yaml

@@ -49,8 +49,6 @@ import_group:
         - https://orcid.org/
     - id: uberon
       module_type: filter
-    - id: cob
-      module_type: filter
     - id: obi
       module_type: filter