Merge pull request #1903 from obophenotype/remove-chebi-odk

Remove CHEBI import from ODK config
obophenotype · Mar 21, 2023 · a7a6140 · a7a6140
2 parents 27aa3ca + f4fb07d
commit a7a6140
Show file tree

Hide file tree

Showing 6 changed files with 163 additions and 18,397 deletions.
diff --git a/docs/odk-workflows/RepositoryFileStructure.md b/docs/odk-workflows/RepositoryFileStructure.md
@@ -21,7 +21,6 @@ These are the current imports in CL
 | 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 |
-| chebi | https://raw.githubusercontent.com/obophenotype/chebi_obo_slim/main/chebi_slim.owl | None |
 | pato | http://purl.obolibrary.org/obo/pato.owl | None |
 | ncbitaxon | http://purl.obolibrary.org/obo/ncbitaxon/subsets/taxslim.owl | None |
 

diff --git a/src/ontology/Makefile b/src/ontology/Makefile
@@ -113,7 +113,7 @@ all_main: $(MAIN_FILES)
 # ----------------------------------------
 
 
-IMPORTS =  pr go caro uberon ro chebi pato ncbitaxon
+IMPORTS =  pr go caro uberon ro pato ncbitaxon
 
 IMPORT_ROOTS =  $(IMPORTDIR)/merged_import
 IMPORT_OWL_FILES = $(foreach n,$(IMPORT_ROOTS), $(n).owl)
@@ -450,15 +450,6 @@ mirror-ro: | $(TMPDIR)
 		$(ROBOT) convert -i $(MIRRORDIR)/ro.owl -o $@.tmp.owl && mv $@.tmp.owl $(TMPDIR)/$@.owl; fi
 
 
-## ONTOLOGY: chebi
-.PHONY: mirror-chebi
-.PRECIOUS: $(MIRRORDIR)/chebi.owl
-mirror-chebi: | $(TMPDIR)
-	if [ $(MIR) = true ] && [ $(IMP) = true ]; then $(ROBOT) convert -I https://raw.githubusercontent.com/obophenotype/chebi_obo_slim/main/chebi_slim.owl -o $@.tmp.owl && \
-		$(ROBOT) remove -i $@.tmp.owl --base-iri $(URIBASE)/CHEBI --axioms external --preserve-structure false --trim false -o $@.tmp.owl &&\
-		mv $@.tmp.owl $(TMPDIR)/$@.owl; fi
-
-
 ## ONTOLOGY: pato
 .PHONY: mirror-pato
 .PRECIOUS: $(MIRRORDIR)/pato.owl

diff --git a/src/ontology/catalog-v001.xml b/src/ontology/catalog-v001.xml
@@ -3,7 +3,6 @@
     <uri id="User Entered Import Resolution" name="http://purl.obolibrary.org/obo/cl.owl" uri="cl-edit.owl"/>
     <uri id="User Entered Import Resolution" name="http://purl.obolibrary.org/obo/cl-plus-zfa.owl" uri="cl-plus-zfa.owl"/>
     <uri id="User Entered Import Resolution" name="http://purl.obolibrary.org/obo/cl-basic.owl" uri="cl-basic.owl"/>
-    <uri id="User Entered Import Resolution" name="http://purl.obolibrary.org/obo/cl/imports/chebi_import.owl" uri="imports/chebi_import.owl"/>
     <uri id="User Entered Import Resolution" name="http://purl.obolibrary.org/obo/cl/imports/uberon_import.owl" uri="imports/uberon_import.owl"/>
     <uri id="User Entered Import Resolution" name="http://purl.obolibrary.org/obo/cl/imports/pr_import.owl" uri="imports/pr_import.owl"/>
     <uri id="User Entered Import Resolution" name="http://purl.obolibrary.org/obo/cl/imports/go_import.owl" uri="imports/go_import.owl"/>

diff --git a/src/ontology/cl-odk.yaml b/src/ontology/cl-odk.yaml
@@ -61,9 +61,6 @@ import_group:
       use_base: TRUE
     - id: ro
       use_base: TRUE
-    - id: chebi
-      make_base: TRUE
-      mirror_from: https://raw.githubusercontent.com/obophenotype/chebi_obo_slim/main/chebi_slim.owl
     - id: pato
       use_base: TRUE
     - id: ncbitaxon

diff --git a/src/ontology/imports/chebi_terms.txt b/src/ontology/imports/chebi_terms.txt