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Resolves #1213

  • docs/ have been added/updated
  • tests have been added/updated
  • mvn verify says all tests pass
  • mvn site says all JavaDocs correct
  • CHANGELOG.md has been updated




<!-- http://www.semanticweb.org/vinicius/ontologies/2024/7/untitled-ontology-2#has_part -->
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These are very ugly IRIs, maybe run a string replace on the file to replace

http://www.semanticweb.org/vinicius/ontologies/2024/7/untitled-ontology-2

with something like

http://example.org/ontology

o.addOption("o", "output", true, "save reasoned ontology to a file");
o.addOption("t", "term", true, "a property to materialize");
o.addOption("T", "term-file", true, "load properties from a file");
o.addOption(
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option should be "false" by default

continue;
}
Set<OWLClassExpression> sces = emr.getSuperClassExpressions(c, true);
Set<OWLClassExpression> sces = emr.getSuperClassExpressions(c, !includeIndirect);
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Ok this seems to make sense! Needs someone from gene ontology reasoner time to check.. @balhoff @cmungall

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Add a --include-indirect option to materialize

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