Merge pull request #10922 from obophenotype/update-import111224

Update import
obophenotype · Dec 11, 2024 · 2a03683 · 2a03683
2 parents 8c21a4e + a37340c
commit 2a03683
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diff --git a/src/ontology/Makefile b/src/ontology/Makefile
@@ -10,7 +10,7 @@
 # More information: https://github.com/INCATools/ontology-development-kit/
 
 # Fingerprint of the configuration file when this Makefile was last generated
-CONFIG_HASH=                96cc08421fe1323e389345fd556c8f1d18ca491947a1f2b227f9c10a39cb0740
+CONFIG_HASH=                0fcd636feea85fce01a9e5009487aad06aedf4ba32833cb10c92bcf68fbc2cc2
 
 
 # ----------------------------------------
@@ -384,7 +384,7 @@ $(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/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*>"  \
+		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/BFO_0000002*>" remove  --select "<http://purl.obolibrary.org/obo/BFO_0000003*>" remove  --select "<http://purl.obolibrary.org/obo/BFO_0000004*>" remove  --select "<http://purl.obolibrary.org/obo/BFO_0000006*>" remove  --select "<http://purl.obolibrary.org/obo/BFO_0000015*>" remove  --select "<http://purl.obolibrary.org/obo/BFO_0000019*>" remove  --select "<http://purl.obolibrary.org/obo/BFO_0000020*>" remove  --select "<http://purl.obolibrary.org/obo/BFO_0000023*>" remove  --select "<http://purl.obolibrary.org/obo/BFO_0000031*>" remove  --select "<http://purl.obolibrary.org/obo/BFO_0000040*>" remove  --select "<http://purl.obolibrary.org/obo/BFO_0000141*>" 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 \
 		remove $(patsubst %, --term %, $(ANNOTATION_PROPERTIES)) -T $(IMPORTDIR)/merged_terms_combined.txt --select complement --select annotation-properties \
 		query --update ../sparql/inject-subset-declaration.ru --update ../sparql/inject-synonymtype-declaration.ru --update ../sparql/postprocess-module.ru \

diff --git a/src/ontology/hp-edit.owl b/src/ontology/hp-edit.owl
@@ -78970,7 +78970,7 @@ AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynony
 AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/HP_0007256> "Pyramidal signs")
 AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/HP_0007256> "Pyramidal tract signs")
 AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> <http://purl.obolibrary.org/obo/HP_0007256> "HP:0007256")
-AnnotationAssertion(rdfs:comment <http://purl.obolibrary.org/obo/HP_0007256> "pyramidal signs are a subset of long-tract signs that specifically indicate corticospinal tract involvement. The more general term long-tract sign refers to  a clinical findings related to damage to the long white matter tracts of the CNS, particularly the corticospinal tract, dorsal columns, and the spinothalamic tract.")
+AnnotationAssertion(rdfs:comment <http://purl.obolibrary.org/obo/HP_0007256> "pyramidal signs are a subset of long-tract signs that specifically indicate corticospinal tract involvement. The more general term long-tract sign refers to a clinical findings related to damage to the long white matter tracts of the CNS, particularly the corticospinal tract, dorsal columns, and the spinothalamic tract.")
 AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/HP_0007256> "Abnormal pyramidal sign")
 EquivalentClasses(<http://purl.obolibrary.org/obo/HP_0007256> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000051> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/PATO_0001624> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000052> <http://purl.obolibrary.org/obo/UBERON_0002707>) ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002573> <http://purl.obolibrary.org/obo/PATO_0000460>))))
 SubClassOf(<http://purl.obolibrary.org/obo/HP_0007256> <http://purl.obolibrary.org/obo/HP_0002423>)

diff --git a/src/ontology/hp-odk.yaml b/src/ontology/hp-odk.yaml
@@ -34,6 +34,17 @@ import_group:
     - <http://purl.obolibrary.org/obo/OBI_*>
     - <http://purl.obolibrary.org/obo/CARO_*>
     - <http://purl.obolibrary.org/obo/ENVO_*>
+    - <http://purl.obolibrary.org/obo/BFO_0000002*>
+    - <http://purl.obolibrary.org/obo/BFO_0000003*>
+    - <http://purl.obolibrary.org/obo/BFO_0000004*>
+    - <http://purl.obolibrary.org/obo/BFO_0000006*>
+    - <http://purl.obolibrary.org/obo/BFO_0000015*>
+    - <http://purl.obolibrary.org/obo/BFO_0000019*>
+    - <http://purl.obolibrary.org/obo/BFO_0000020*>
+    - <http://purl.obolibrary.org/obo/BFO_0000023*>
+    - <http://purl.obolibrary.org/obo/BFO_0000031*>
+    - <http://purl.obolibrary.org/obo/BFO_0000040*>
+    - <http://purl.obolibrary.org/obo/BFO_0000141*>
     - <http://purl.obolibrary.org/obo/SO_*>
     - <http://purl.obolibrary.org/obo/cl#abbreviation*>
     - <http://purl.obolibrary.org/obo/cl#added_for_HCA*>