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Add unmerge step to take out problem axioms. #151

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May 27, 2024
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Add unmerge step to take out problem axioms. #151

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6 changes: 3 additions & 3 deletions Makefile
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Original file line number Diff line number Diff line change
Expand Up @@ -199,13 +199,13 @@ oarcs-base.owl: oarcs.owl
--trim false \
--output $@

ontologies-merged.ttl: mirror
ontologies-merged.ttl: mirror unmerge.ofn
$(ROBOT) merge $(addprefix -i mirror/,$(shell ls mirror)) \
remove --axioms 'disjoint' --trim true --preserve-structure false \
remove --term 'owl:Nothing' --trim true --preserve-structure false \
query --update build-sparql/filter-bad-uri-values.ru \
unmerge -i unmerge.ofn \
reason -r ELK -D debug.ofn -o [email protected] &&\
$(RIOT) -q --nocheck --stream=ntriples [email protected] >$@
$(RIOT) -q --nocheck --output=turtle [email protected] >$@

ontologies-merged.ofn.gz: ontologies-merged.ttl
$(ROBOT) convert -i $< -o ontologies-merged.ofn && gzip ontologies-merged.ofn
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18 changes: 18 additions & 0 deletions unmerge.ofn
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@@ -0,0 +1,18 @@
Prefix(:=<http://purl.obolibrary.org/obo/go.owl#>)
Prefix(dc:=<http://purl.org/dc/elements/1.1/>)
Prefix(go:=<http://purl.obolibrary.org/obo/go#>)
Prefix(obo:=<http://purl.obolibrary.org/obo/>)
Prefix(owl:=<http://www.w3.org/2002/07/owl#>)
Prefix(rdf:=<http://www.w3.org/1999/02/22-rdf-syntax-ns#>)
Prefix(xml:=<http://www.w3.org/XML/1998/namespace>)
Prefix(xsd:=<http://www.w3.org/2001/XMLSchema#>)
Prefix(obo1:=<http://www.geneontology.org/formats/oboInOwl#http://purl.obolibrary.org/obo/>)
Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)
Prefix(terms:=<http://purl.org/dc/terms/>)
Prefix(terms2:=<http://www.geneontology.org/formats/oboInOwl#http://purl.org/dc/terms/>)
Prefix(oboInOwl:=<http://www.geneontology.org/formats/oboInOwl#>)


Ontology(
AnnotationAssertion(obo:IAO_0000233 obo:GO_0034512 "- [ ] box C/D RNA 5'-end processing -> box C/D sno(s)RNA 5'-end processing"^^xsd:anyURI)
)
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