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Get rid of partof cycles #314
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@@ -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.
@@ -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 \ | |||
materialize -T basic_properties.txt \ |
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We do this a bit later now.
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.
remove --term PR:000000001 \ | ||
--term SO:0000252 \ | ||
--term SO:0000234 \ | ||
reason --reasoner ELK --equivalent-classes-allowed none --exclude-tautologies structural \ |
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This is only for QC purposes.
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- I have created two mock releases with or without the changes, respectively, in this PR.
oba.owl with the changes contains a lot more axioms of the type
- SubClassOf(<http://purl.obolibrary.org/obo/XX_12345678> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> <...>)
that are related to part of
something.
2. I have also checked the oba.owl
release products in Protege carefully looking for major differences or problems in the two versions, but other than the extra part of
-type subclasses (which make sense) I could not find anything outstanding.
🎉
THANKS! Feel free to merge, and when all other PRs are processed, create a release! Thank you so much for checking! |
Fixes #313.
This PR ensures that we never release OBA again with subclass of cycles (as a consequence of relaxing owl:equivalentClasses).
Depends on
@rays22 can you take this PR over? It is basically done. Remaining tasks: