Merge pull request #3154 from obophenotype/use-sssom-to-apply-import-…

…corrections Use SSSOM to correct local imports when needed.
obophenotype · Dec 21, 2023 · bc6a319 · bc6a319
2 parents d729acf + 08c91d9
commit bc6a319
Show file tree

Hide file tree

Showing 4 changed files with 56 additions and 49 deletions.
diff --git a/src/ontology/imports/map-mouse-stages.tsv b/src/ontology/imports/map-mouse-stages.tsv
diff --git a/src/ontology/imports/map-properties.tsv b/src/ontology/imports/map-properties.tsv
diff --git a/src/ontology/mappings/import-corrections.sssom.tsv b/src/ontology/mappings/import-corrections.sssom.tsv
@@ -0,0 +1,50 @@
+#curie_map:
+#  BFO: "http://purl.obolibrary.org/obo/BFO_"
+#  EMAPA: "http://purl.obolibrary.org/obo/emapa#"
+#  IAO: "http://purl.obolibrary.org/obo/IAO_"
+#  MA: "http://purl.obolibrary.org/obo/ma#"
+#  MmusDv: "http://purl.obolibrary.org/obo/MmusDv_"
+#  RO: "http://purl.obolibrary.org/obo/RO_"
+#  TS: "http://purl.obolibrary.org/obo/TS_"
+#  XAO: "http://purl.obolibrary.org/obo/xao#"
+#mapping_set_id: "http://purl.obolibrary.org/obo/uberon/import-corrections.sssom.tsv"
+#mapping_set_description: "Terms and properties to replace in imported ontologies."
+#license: "http://creativecommons.org/licenses/by/3.0/"
+#mapping_date: "2023-12-11"
+subject_id	predicate_id	object_id	mapping_justification
+TS:01	IAO:0100001	MmusDv:0000003	semapv:ManualMappingCuration
+TS:02	IAO:0100001	MmusDv:0000005	semapv:ManualMappingCuration
+TS:03	IAO:0100001	MmusDv:0000006	semapv:ManualMappingCuration
+TS:04	IAO:0100001	MmusDv:0000008	semapv:ManualMappingCuration
+TS:05	IAO:0100001	MmusDv:0000009	semapv:ManualMappingCuration
+TS:06	IAO:0100001	MmusDv:0000010	semapv:ManualMappingCuration
+TS:07	IAO:0100001	MmusDv:0000011	semapv:ManualMappingCuration
+TS:08	IAO:0100001	MmusDv:0000012	semapv:ManualMappingCuration
+TS:09	IAO:0100001	MmusDv:0000014	semapv:ManualMappingCuration
+TS:10	IAO:0100001	MmusDv:0000015	semapv:ManualMappingCuration
+TS:11	IAO:0100001	MmusDv:0000017	semapv:ManualMappingCuration
+TS:12	IAO:0100001	MmusDv:0000019	semapv:ManualMappingCuration
+TS:13	IAO:0100001	MmusDv:0000020	semapv:ManualMappingCuration
+TS:14	IAO:0100001	MmusDv:0000021	semapv:ManualMappingCuration
+TS:15	IAO:0100001	MmusDv:0000022	semapv:ManualMappingCuration
+TS:16	IAO:0100001	MmusDv:0000023	semapv:ManualMappingCuration
+TS:17	IAO:0100001	MmusDv:0000024	semapv:ManualMappingCuration
+TS:18	IAO:0100001	MmusDv:0000025	semapv:ManualMappingCuration
+TS:19	IAO:0100001	MmusDv:0000026	semapv:ManualMappingCuration
+TS:20	IAO:0100001	MmusDv:0000027	semapv:ManualMappingCuration
+TS:21	IAO:0100001	MmusDv:0000028	semapv:ManualMappingCuration
+TS:22	IAO:0100001	MmusDv:0000029	semapv:ManualMappingCuration
+TS:23	IAO:0100001	MmusDv:0000032	semapv:ManualMappingCuration
+TS:24	IAO:0100001	MmusDv:0000033	semapv:ManualMappingCuration
+TS:25	IAO:0100001	MmusDv:0000034	semapv:ManualMappingCuration
+TS:26	IAO:0100001	MmusDv:0000035	semapv:ManualMappingCuration
+TS:27	IAO:0100001	MmusDv:0000036	semapv:ManualMappingCuration
+TS:28	IAO:0100001	MmusDv:0000043	semapv:ManualMappingCuration
+EMAPA:develops_from	IAO:0100001	RO:0002202	semapv:ManualMappingCuration
+EMAPA:ends_at	IAO:0100001	RO:0002497	semapv:ManualMappingCuration
+EMAPA:part_of	IAO:0100001	BFO:0000050	semapv:ManualMappingCuration
+EMAPA:starts_at	IAO:0100001	RO:0002496	semapv:ManualMappingCuration
+MA:part_of	IAO:0100001	BFO:0000050	semapv:ManualMappingCuration
+XAO:end_stage	IAO:0100001	RO:0002497	semapv:ManualMappingCuration
+XAO:preceded_by	IAO:0100001	RO:0002087	semapv:ManualMappingCuration
+XAO:start_stage	IAO:0100001	RO:0002496	semapv:ManualMappingCuration
diff --git a/src/ontology/uberon.Makefile b/src/ontology/uberon.Makefile
@@ -424,25 +424,20 @@ imports/local-ssso.owl: mirror/ssso.owl
 # external entities we also need to replace some old-style properties.
 # ----------------------------------------
 # EMAPA also needs translation between TS-style stages to MmusDv stages
-imports/local-emapa.owl: mirror/emapa.owl $(IMPORTDIR)/map-properties.tsv
-	$(ROBOT) rename -i $< --mappings $(IMPORTDIR)/map-properties.tsv \
-		        --allow-missing-entities true --allow-duplicates true \
-		 rename --mappings $(IMPORTDIR)/map-mouse-stages.tsv \
-		        --allow-missing-entities true \
+imports/local-emapa.owl: mirror/emapa.owl mappings/import-corrections.sssom.tsv $(TMPDIR)/plugins/sssom.jar
+	$(ROBOT) sssom:rename -i $< --sssom mappings/import-corrections.sssom.tsv \
 		 remove --base-iri $(URIBASE)/EMAPA_ --axioms external \
 		        --preserve-structure false --trim false \
 		 convert -f ofn -o $@
 
-imports/local-ma.owl: mirror/ma.owl $(IMPORTDIR)/map-properties.tsv
-	$(ROBOT) rename -i $< --mappings $(IMPORTDIR)/map-properties.tsv \
-		        --allow-missing-entities true --allow-duplicates true \
+imports/local-ma.owl: mirror/ma.owl mappings/import-corrections.sssom.tsv $(TMPDIR)/plugins/sssom.jar
+	$(ROBOT) sssom:rename -i $< --sssom mappings/import-corrections.sssom.tsv \
 		 remove --base-iri $(URIBASE)/MA_ --axioms external \
 		        --preserve-structure false --trim false \
 		 convert -f ofn -o $@
 
-imports/local-xao.owl: mirror/xao.owl $(IMPORTDIR)/map-properties.tsv
-	$(ROBOT) rename -i $< --mappings $(IMPORTDIR)/map-properties.tsv \
-		        --allow-missing-entities true --allow-duplicates true \
+imports/local-xao.owl: mirror/xao.owl mappings/import-corrections.sssom.tsv $(TMPDIR)/plugins/sssom.jar
+	$(ROBOT) sssom:rename -i $< --sssom mappings/import-corrections.sssom.tsv \
 		 remove --base-iri $(URIBASE)/XAO_ --axioms external \
 		        --preserve-structure false --trim false \
 		 convert -f ofn -o $@