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Update import #10922

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merged 3 commits into from
Dec 11, 2024
Merged

Update import #10922

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a3f3f03
Remove BFO from imports
matentzn Dec 11, 2024
88fd57f
Refresh imports
matentzn Dec 11, 2024
a37340c
Removing double space from hp-edit to pass tests
matentzn Dec 11, 2024
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4 changes: 2 additions & 2 deletions src/ontology/Makefile
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Original file line number Diff line number Diff line change
Expand Up @@ -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


# ----------------------------------------
Expand Down Expand Up @@ -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 \
Expand Down
2 changes: 1 addition & 1 deletion src/ontology/hp-edit.owl
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Expand Up @@ -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>)
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11 changes: 11 additions & 0 deletions src/ontology/hp-odk.yaml
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Expand Up @@ -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*>
Expand Down
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