Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

create skeleton for adding indirect existentials in materialize #1215

Draft
wants to merge 1 commit into
base: master
Choose a base branch
from

Conversation

souzadevinicius
Copy link

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 -->
Copy link
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

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

@@ -44,6 +44,8 @@ public MaterializeCommand() {
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(
Copy link
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

option should be "false" by default

@@ -143,7 +169,7 @@ public static void materialize(
logger.debug("Excluding classes not in main ontology: " + c);
continue;
}
Set<OWLClassExpression> sces = emr.getSuperClassExpressions(c, true);
Set<OWLClassExpression> sces = emr.getSuperClassExpressions(c, !includeIndirect);
Copy link
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Ok this seems to make sense! Needs someone from gene ontology reasoner time to check.. @balhoff @cmungall

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

Successfully merging this pull request may close these issues.

Add a --include-indirect option to materialize
2 participants