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Filter out dangling gene IRIs in imports #3379

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merged 2 commits into from
Oct 15, 2024
Merged

Filter out dangling gene IRIs in imports #3379

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bab8c69
Filter out dangling gene IRIs.
gouttegd Oct 15, 2024
5694045
Commit re-generated Makefile.
gouttegd Oct 15, 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= 943829f9eb8e1b8d46bf5f3f878364bb18f10e0d9eee11d7c28bfb3dfba894c7
CONFIG_HASH= 60e47a069bd32a71a48c480dcf88b75d116c5eef7d1f9a55073500ff79968b28


# ----------------------------------------
Expand Down Expand Up @@ -391,7 +391,7 @@ $(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://www.informatics.jax.org/marker/MGI:*>" remove --select "<http://purl.obolibrary.org/obo/OBA_*>" remove --select "<http://purl.obolibrary.org/obo/ENVO_*>" remove --select "<http://purl.obolibrary.org/obo/OBI_*>" remove --select "<http://purl.obolibrary.org/obo/GOCHE_*>" remove --select "<http://www.genenames.org/cgi-bin/gene_symbol_report*>" \
remove --select "<http://www.informatics.jax.org/marker/MGI:*>" remove --select "<http://purl.obolibrary.org/obo/OBA_*>" remove --select "<http://purl.obolibrary.org/obo/ENVO_*>" remove --select "<http://purl.obolibrary.org/obo/OBI_*>" remove --select "<http://purl.obolibrary.org/obo/GOCHE_*>" remove --select "<http://www.genenames.org/cgi-bin/gene_symbol_report*>" remove --select "<http://www.ncbi.nlm.nih.gov/gene/*>" remove --select "<http://birdgenenames.org/cgnc/GeneReport*>" \
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 \
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2 changes: 2 additions & 0 deletions src/ontology/uberon-odk.yaml
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Expand Up @@ -42,6 +42,8 @@ import_group:
- <http://purl.obolibrary.org/obo/OBI_*>
- <http://purl.obolibrary.org/obo/GOCHE_*>
- <http://www.genenames.org/cgi-bin/gene_symbol_report*>
- <http://www.ncbi.nlm.nih.gov/gene/*>
- <http://birdgenenames.org/cgnc/GeneReport*>
products:
- id: pr
make_base: TRUE
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