feat(gen-owl): honor instantiates on emitted schema resources - #4171

Summary

gen-owl ignored instantiates. It now asserts each declared membership as rdf:type on the emitted resource of the schema, a class, a slot, a locally emitted type, an enum or a non-literal permissible value.

enums:
  LinkCategory:
    implements: [owl:NamedIndividual]
    permissible_values:
      isLicense:
        meaning: ex:isLicense
        instantiates: [vocab:LicenseCategory]

ex:isLicense a owl:NamedIndividual, ex:LinkCategory, vocab:LicenseCategory .
vocab:LicenseCategory a owl:Class .

• The membership types the element itself, not its data instances: no rdfs:subClassOf, no inherited slots (instantiation guide). An enum of named individuals keeps its own owl:oneOf; the external class stays open.
• Skipped with a warning: a permissible value rendered as a literal, which can't be a subject; a resource in the OWL 2 reserved vocabulary, such as a type emitted as xsd:integer, which can't be an individual (Structural Specification §2.4); and a value that is neither a CURIE nor an IRI, which would become a relative IRI.
• With use_native_uris=False the assertion goes on the class_uri resource, like every other axiom about the element.
• The instantiated class is declared as owl:Class, since OWL 2 DL requires a declaration for every class a class assertion uses (§5.8.1). An OWLAPI 5.5.0 profile check of the output flagged the missing declaration.

Why

The specification (05validation.md, annotation validation) defines instantiates as a uriorcurie "that references a class that serves as a metamodel extension class". #153 asked for a way to make "instances of linkml classes … OWL classes" and was closed with "The metamodel now has instantiates". In OWL's RDF mapping a class assertion is rdf:type (OWL 2 Mapping to RDF). No new option: the schema already states the relationship.

Other generators

gen-rdf and gen-jsonld serialize the schema as metamodel data and keep linkml:instantiates, as an xsd:anyURI literal holding the CURIE, as for every uriorcurie metaslot. JSON Schema and SHACL describe data instances, which the element's metaclass doesn't type.

How was this tested?

test_owlgen.py: several memberships, minted and explicit IRIs, permissible values as individuals and as classes, every element kind with both metaclasses and type_objects values, both URI modes, the three skip cases, and gen-rdf versus gen-owl. 123 passed locally; CI on the head.

Areas of uncertainty

• Punning under --no-metaclasses: rdf:type on a class, slot or type puns the IRI as an individual even with --no-metaclasses, the default, which keeps LinkML's own metamodel types out. OWL 2 DL permits this punning (Metamodeling), and instantiates is the author's own statement, so it is honoured regardless. Is that the reading you want, or should explicit memberships follow --metaclasses too?

Fork review: ASCS-eV#31.

Checklist

• My code follows the contributor guidelines
• I have added tests that prove my fix/feature works
• Existing tests pass locally with my changes

AI Assistance

If you used AI tools while preparing this PR, you are still the author and responsible for understanding, verifying, and defending your submission. Please engage with reviewers personally rather than through your agent during feedback and revisions. See our AI Covenant for details.