Merge pull request #10250 from obophenotype/remove-cl-uberon-properties

Remove cl uberon annotation properties
obophenotype · Dec 10, 2023 · a321b69 · a321b69
2 parents 5d8ec1f + 5dd59c0
commit a321b69
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Showing 3 changed files with 3,465 additions and 4,885 deletions.
diff --git a/src/ontology/Makefile b/src/ontology/Makefile
@@ -322,7 +322,7 @@ $(IMPORTDIR)/merged_terms_combined.txt: $(ALL_TERMS_COMBINED)
 
 $(IMPORTDIR)/merged_import.owl: $(MIRRORDIR)/merged.owl $(IMPORTDIR)/merged_terms_combined.txt
 	if [ $(IMP) = true ]; then $(ROBOT) merge -i $< \
-		remove  --select "<http://purl.obolibrary.org/obo/GOCHE_*>" remove  --select "<http://purl.obolibrary.org/obo/NCBITaxon_Union_*>" remove  --select "<http://purl.obolibrary.org/obo/NCBITaxon_*>" remove  --select "<http://www.informatics.jax.org/marker/MGI:*>" remove  --select "<http://purl.obolibrary.org/obo/OBI_*>" remove  --select "<http://purl.obolibrary.org/obo/CARO_*>" remove  --select "<http://purl.obolibrary.org/obo/ENVO_*>" remove  --select "<http://purl.obolibrary.org/obo/SO_*>"  \
+		remove  --select "<http://purl.obolibrary.org/obo/GOCHE_*>" remove  --select "<http://purl.obolibrary.org/obo/NCBITaxon_Union_*>" remove  --select "<http://purl.obolibrary.org/obo/NCBITaxon_*>" remove  --select "<http://www.informatics.jax.org/marker/MGI:*>" remove  --select "<http://purl.obolibrary.org/obo/OBI_*>" remove  --select "<http://purl.obolibrary.org/obo/CARO_*>" remove  --select "<http://purl.obolibrary.org/obo/ENVO_*>" remove  --select "<http://purl.obolibrary.org/obo/SO_*>" remove  --select "<http://purl.obolibrary.org/obo/cl#abbreviation*>" remove  --select "<http://purl.obolibrary.org/obo/cl#added_for_HCA*>" remove  --select "<http://purl.obolibrary.org/obo/uberon/core#ABBREVIATION*>" remove  --select "<http://purl.obolibrary.org/obo/uberon/core#COMPARATIVE_PREFERRED*>" remove  --select "<http://purl.obolibrary.org/obo/uberon/core#DEPRECATED*>" remove  --select "<http://purl.obolibrary.org/obo/uberon/core#DUBIOUS*>" remove  --select "<http://purl.obolibrary.org/obo/uberon/core#HOMOLOGY*>" remove  --select "<http://purl.obolibrary.org/obo/uberon/core#HUMAN_PREFERRED*>" remove  --select "<http://purl.obolibrary.org/obo/uberon/core#INCONSISTENT*>" remove  --select "<http://purl.obolibrary.org/obo/uberon/core#LATIN*>" remove  --select "<http://purl.obolibrary.org/obo/uberon/core#MISSPELLING*>" remove  --select "<http://purl.obolibrary.org/obo/uberon/core#NON_AMNIOTE*>" remove  --select "<http://purl.obolibrary.org/obo/uberon/core#NON_MAMMAL*>" remove  --select "<http://purl.obolibrary.org/obo/uberon/core#PENDING_REVIEW*>" remove  --select "<http://purl.obolibrary.org/obo/uberon/core#PLURAL*>" remove  --select "<http://purl.obolibrary.org/obo/uberon/core#SENSU*>" remove  --select "<http://purl.obolibrary.org/obo/uberon/core#SYSTEMATIC*>"  \
 		extract -T $(IMPORTDIR)/merged_terms_combined.txt --force true --copy-ontology-annotations true --individuals exclude --method BOT \
 		query --update ../sparql/inject-subset-declaration.ru --update ../sparql/inject-synonymtype-declaration.ru --update ../sparql/postprocess-module.ru \
 		$(ANNOTATE_CONVERT_FILE); fi

diff --git a/src/ontology/hp-odk.yaml b/src/ontology/hp-odk.yaml
@@ -30,6 +30,23 @@ import_group:
     - <http://purl.obolibrary.org/obo/CARO_*>
     - <http://purl.obolibrary.org/obo/ENVO_*>
     - <http://purl.obolibrary.org/obo/SO_*>
+    - <http://purl.obolibrary.org/obo/cl#abbreviation*>
+    - <http://purl.obolibrary.org/obo/cl#added_for_HCA*>
+    - <http://purl.obolibrary.org/obo/uberon/core#ABBREVIATION*>
+    - <http://purl.obolibrary.org/obo/uberon/core#COMPARATIVE_PREFERRED*>
+    - <http://purl.obolibrary.org/obo/uberon/core#DEPRECATED*>
+    - <http://purl.obolibrary.org/obo/uberon/core#DUBIOUS*>
+    - <http://purl.obolibrary.org/obo/uberon/core#HOMOLOGY*>
+    - <http://purl.obolibrary.org/obo/uberon/core#HUMAN_PREFERRED*>
+    - <http://purl.obolibrary.org/obo/uberon/core#INCONSISTENT*>
+    - <http://purl.obolibrary.org/obo/uberon/core#LATIN*>
+    - <http://purl.obolibrary.org/obo/uberon/core#MISSPELLING*>
+    - <http://purl.obolibrary.org/obo/uberon/core#NON_AMNIOTE*>
+    - <http://purl.obolibrary.org/obo/uberon/core#NON_MAMMAL*>
+    - <http://purl.obolibrary.org/obo/uberon/core#PENDING_REVIEW*>
+    - <http://purl.obolibrary.org/obo/uberon/core#PLURAL*>
+    - <http://purl.obolibrary.org/obo/uberon/core#SENSU*>
+    - <http://purl.obolibrary.org/obo/uberon/core#SYSTEMATIC*>
   slme_individuals: exclude
   mirror_max_time_download: 400
   products: