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Remove unneeded HGNC SPARQL updates #459

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merged 2 commits into from
Mar 11, 2024
Merged

Remove unneeded HGNC SPARQL updates #459

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481d20d
Unneeded HGNC SPARQL
joeflack4 Mar 3, 2024
d189132
Unneeded HGNC SPARQL
joeflack4 Mar 10, 2024
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4 changes: 0 additions & 4 deletions src/ontology/mondo-ingest.Makefile
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Original file line number Diff line number Diff line change
Expand Up @@ -70,7 +70,6 @@ $(COMPONENTSDIR)/omim.owl: $(TMPDIR)/omim_relevant_signature.txt | component-dow
query \
--update ../sparql/fix_omimps.ru \
--update ../sparql/fix-labels-with-brackets.ru \
--update ../sparql/fix_hgnc_mappings.ru \
--update ../sparql/fix_complex_reification.ru \
--update ../sparql/fix_illegal_punning_omim.ru \
annotate --ontology-iri $(URIBASE)/mondo/sources/omim.owl --version-iri $(URIBASE)/mondo/sources/$(TODAY)/omim.owl -o $@; fi
Expand Down Expand Up @@ -113,7 +112,6 @@ $(COMPONENTSDIR)/doid.owl: $(TMPDIR)/doid_relevant_signature.txt | component-dow
remove -T $(TMPDIR)/doid_relevant_signature.txt --select complement --select "classes individuals" --trim false \
query \
--update ../sparql/fix_omimps.ru \
--update ../sparql/fix_hgnc_mappings.ru \
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@joeflack4 joeflack4 Mar 3, 2024 •
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File Rename File & ref deletion

If indeed I'm correct and fix_hgnc_mappings.ru only applies to OMIM, why don't we prepend omim_ to the file name for disambiguation?

Additional FYI

I also found a similar situation with an ORDO related query.

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You could, but even better: is this "fix" still necessary? Maybe it can be removed altogether?

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That's a good question. I'll look into that.

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Is this still an open action item, to look into whether the "fix" hgnc mappings is still necessary?

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yep

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@matentzn You were correct. I ran with and without this SPARQL update, and there was no difference. I've deleted the file and its references. Feel free to merge!

--update ../sparql/fix-labels-with-brackets.ru \
--update ../sparql/fix_complex_reification.ru \
--update ../sparql/rm_xref_by_prefix.ru \
Expand Down Expand Up @@ -143,7 +141,6 @@ $(COMPONENTSDIR)/icd10cm.owl: $(TMPDIR)/icd10cm_relevant_signature.txt | compone
query \
--update ../sparql/fix_omimps.ru \
--update ../sparql/fix-labels-with-brackets.ru \
--update ../sparql/fix_hgnc_mappings.ru \
--update ../sparql/fix_complex_reification.ru \
remove -T config/properties.txt --select complement --select properties --trim true \
annotate --ontology-iri $(URIBASE)/mondo/sources/icd10cm.owl --version-iri $(URIBASE)/mondo/sources/$(TODAY)/icd10cm.owl -o $@; fi
Expand All @@ -158,7 +155,6 @@ $(COMPONENTSDIR)/icd10who.owl: $(TMPDIR)/icd10who_relevant_signature.txt | compo
query \
--update ../sparql/fix_omimps.ru \
--update ../sparql/fix-labels-with-brackets.ru \
--update ../sparql/fix_hgnc_mappings.ru \
--update ../sparql/fix_complex_reification.ru \
remove -T config/properties.txt --select complement --select properties --trim true \
annotate --ontology-iri $(URIBASE)/mondo/sources/icd10who.owl --version-iri $(URIBASE)/mondo/sources/$(TODAY)/icd10who.owl -o $@; fi
Expand Down
40 changes: 0 additions & 40 deletions src/sparql/fix_hgnc_mappings.ru
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