Fix ncbitaxon

berkeleybop · Feb 25, 2023 · 60282a2 · 60282a2
1 parent 54bd007
commit 60282a2
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Showing 3 changed files with 8 additions and 3 deletions.
diff --git a/src/ontology/Makefile b/src/ontology/Makefile
@@ -434,7 +434,7 @@ mirror-chebi: | $(TMPDIR)
 mirror-ncbitaxon: | $(TMPDIR)
 	if [ $(MIR) = true ] && [ $(IMP) = true ] && [ $(IMP_LARGE) = true ]; then curl -L $(OBOBASE)/ncbitaxon.owl.gz --create-dirs -o $(MIRRORDIR)/ncbitaxon.owl.gz --retry 4 --max-time 200 &&\
 		$(ROBOT) convert -i $(MIRRORDIR)/ncbitaxon.owl.gz -o $@.tmp.owl && \
-		$(ROBOT) remove -i $@.tmp.owl --base-iri $(URIBASE)/NCBITAXON --axioms external --preserve-structure false --trim false -o $@.tmp.owl &&\
+		$(ROBOT) remove -i $@.tmp.owl --base-iri http://purl.obolibrary.org/obo/NCBITaxon_ --axioms external --preserve-structure false --trim false -o $@.tmp.owl &&\
 		mv $@.tmp.owl $(TMPDIR)/$@.owl; fi
 
 

diff --git a/src/ontology/bero-odk.yaml b/src/ontology/bero-odk.yaml
@@ -32,6 +32,8 @@ import_group:
       is_large: TRUE
       use_gzipped: TRUE
       make_base: TRUE
+      base_iris:
+        - http://purl.obolibrary.org/obo/NCBITaxon_
     - id: envo
       use_base: TRUE
     - id: go

diff --git a/src/ontology/bero.Makefile b/src/ontology/bero.Makefile
@@ -71,8 +71,11 @@ $(IMPORTDIR)/obi_import.owl: $(MIRRORDIR)/obi.owl $(IMPORTDIR)/obi_terms_combine
 		annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) --output $@.tmp.owl && mv $@.tmp.owl $@; fi
 
 $(IMPORTDIR)/ncbitaxon_import.owl: $(MIRRORDIR)/ncbitaxon.owl $(IMPORTDIR)/ncbitaxon_terms_combined.txt
-	if [ $(IMP) = true ] && [ $(IMP_LARGE) = true ]; then $(ROBOT) merge -i $<  \
-	remove --term "http://purl.obolibrary.org/obo/ncbitaxon#genbank_common_name" --term "http://purl.obolibrary.org/obo/ncbitaxon#common_name" --term "oboInOwl:hasOBONamespace" --term "oboInOwl:hasDbXref" --term "ncbitaxon:has_rank" \
+	if [ $(IMP) = true ] && [ $(IMP_LARGE) = true ]; then $(ROBOT) merge -i $(MIRRORDIR)/ncbitaxon.owl  \
+	remove --term "oboInOwl:hasOBONamespace" \
+		--term "oboInOwl:hasDbXref" \
+		--term "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId" \
+		--term "http://purl.obolibrary.org/obo/ncbitaxon#has_rank" \
     $(ANNOTATE_CONVERT_FILE); fi
 
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