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Get rid of partof cycles #314

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merged 10 commits into from
May 10, 2024
Merged

Get rid of partof cycles #314

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6e22f0b
Get rid of partof cycles
matentzn Feb 19, 2024
2045c1a
Update oba.obo
matentzn Feb 19, 2024
a21330a
Update oba.obo
matentzn Feb 22, 2024
fd09f99
Update oba.Makefile
matentzn Feb 22, 2024
db0d66c
Merge branch 'master' into part-of-cycles
matentzn May 5, 2024
db11656
Update oba.Makefile
matentzn May 5, 2024
f1a83c4
Remove reflexivity axiom
matentzn May 5, 2024
57135b7
Merge branch 'master' into part-of-cycles
matentzn May 5, 2024
988f732
Merge branch 'update-imports' into part-of-cycles
matentzn May 5, 2024
c2570d9
Merge branch 'master' into part-of-cycles
rays22 May 9, 2024
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3 changes: 0 additions & 3 deletions src/ontology/components/reasoner_axioms.owl
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11 changes: 7 additions & 4 deletions src/ontology/oba.Makefile
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Original file line number Diff line number Diff line change
Expand Up @@ -81,12 +81,15 @@ $(MIRRORDIR)/lipidmaps.owl: $(TEMPLATEDIR)/lipidmaps.tsv
$(ONT)-full.owl: $(SRC) $(OTHER_SRC)
echo "INFO: Running FULL release, which is customised for OBA."
$(ROBOT) merge --input $< \
merge -i components/reasoner_axioms.owl \
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This is removing the following axiom:

ReflexiveObjectProperty(<http://purl.obolibrary.org/obo/BFO_0000050>)

Due to the global properties of this statement, we are dropping it.

materialize -T basic_properties.txt \
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We do this a bit later now.

reason --reasoner ELK --equivalent-classes-allowed all --exclude-tautologies structural \
reason --reasoner ELK --equivalent-classes-allowed asserted-only --exclude-tautologies structural \
remove --term PR:000000001 \
--term SO:0000252 \
--term SO:0000234 \
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We remove a number of asserted equivalent classes forcefully. All three terms have equivalent classes that we are preserving.

reason --reasoner ELK --equivalent-classes-allowed none --exclude-tautologies structural \
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This is only for QC purposes.

relax \
reduce -r ELK \
unmerge -i components/reasoner_axioms.owl \
materialize -T basic_properties.txt \
reduce -r ELK \
$(SHARED_ROBOT_COMMANDS) annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) --output [email protected] && mv [email protected] $@

# Synonyms are managed on Google Sheets
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