remove caro (#2199)

Co-authored-by: Anita Caron <[email protected]>

docs/odk-workflows/RepositoryFileStructure.md

@@ -18,7 +18,6 @@ These are the current imports in CL
 | ------ | --- | ---- |
 | pr | https://raw.githubusercontent.com/obophenotype/pro_obo_slim/master/pr_slim.owl | None |
 | go | http://purl.obolibrary.org/obo/go.owl | None |
-| caro | http://purl.obolibrary.org/obo/caro.owl | None |
 | uberon | http://purl.obolibrary.org/obo/uberon.owl | None |
 | ro | http://purl.obolibrary.org/obo/ro.owl | None |
 | pato | http://purl.obolibrary.org/obo/pato.owl | None |

src/ontology/Makefile

@@ -1,7 +1,7 @@
 # ----------------------------------------
 # Makefile for cl
 # Generated using ontology-development-kit
-# ODK Version: v1.4.1
+# ODK Version: v1.4.3
 # ----------------------------------------
 # IMPORTANT: DO NOT EDIT THIS FILE. To override default make goals, use cl.Makefile instead
 
@@ -43,7 +43,7 @@ REPORT_PROFILE_OPTS =
 OBO_FORMAT_OPTIONS =        
 SPARQL_VALIDATION_CHECKS =  equivalent-classes owldef-self-reference nolabels pmid-not-dbxref obsolete-replaced_by obsolete-alt-id orcid-contributor illegal-annotation-property label-synonym-polysemy 
 SPARQL_EXPORTS =            basic-report 
-ODK_VERSION_MAKEFILE =      v1.4.1
+ODK_VERSION_MAKEFILE =      v1.4.3
 
 TODAY ?=                    $(shell date +%Y-%m-%d)
 OBODATE ?=                  $(shell date +'%d:%m:%Y %H:%M')
@@ -113,7 +113,7 @@ all_main: $(MAIN_FILES)
 # ----------------------------------------
 
 
-IMPORTS =  pr go caro uberon ro pato ncbitaxon omo
+IMPORTS =  pr go uberon ro pato ncbitaxon omo
 
 IMPORT_ROOTS =  $(IMPORTDIR)/merged_import
 IMPORT_OWL_FILES = $(foreach n,$(IMPORT_ROOTS), $(n).owl)
@@ -456,14 +456,6 @@ mirror-go: | $(TMPDIR)
 		$(ROBOT) convert -i $(MIRRORDIR)/go.owl -o $@.tmp.owl && mv $@.tmp.owl $(TMPDIR)/$@.owl; fi
 
 
-## ONTOLOGY: caro
-.PHONY: mirror-caro
-.PRECIOUS: $(MIRRORDIR)/caro.owl
-mirror-caro: | $(TMPDIR)
-	if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/caro/caro-base.owl --create-dirs -o $(MIRRORDIR)/caro.owl --retry 4 --max-time 200 &&\
-		$(ROBOT) convert -i $(MIRRORDIR)/caro.owl -o $@.tmp.owl && mv $@.tmp.owl $(TMPDIR)/$@.owl; fi
-
-
 ## ONTOLOGY: uberon
 .PHONY: mirror-uberon
 .PRECIOUS: $(MIRRORDIR)/uberon.owl

src/ontology/cl-odk.yaml

@@ -58,8 +58,6 @@ import_group:
         - http://purl.obolibrary.org/obo/GO_
         - http://purl.obolibrary.org/obo/GOREL_
         - http://purl.obolibrary.org/obo/GOCHE_
-    - id: caro
-      use_base: TRUE
     - id: uberon 
       use_base: TRUE
     - id: ro