Fix validation to recognize mixin classes as valid node categories

[Copilot]

KGX validation incorrectly flagged mixin classes like biolink:GenomicEntity as invalid node categories. This occurred because BMT's get_descendants() returns only classes with is_a/mixin relationships, not the mixin classes themselves.

Changes

• Added helper method _collect_valid_uris_with_mixins(): Single-pass collection of URIs from descendants and their referenced mixins, reducing complexity from O(n*m) to O(n+m)

• Updated _get_valid_categories() and _get_valid_predicates(): Now include mixin classes that are actually used by descendants

• Added tests: Verify GenomicEntity and other mixins are recognized as valid categories

Example

Before this fix, nodes with mixin categories were flagged:

{
    'id': 'HGNC:1234',
    'category': ['biolink:GenomicEntity'],  # ❌ Invalid warning
    'name': 'Test Gene'
}

After:

{
    'id': 'HGNC:1234', 
    'category': ['biolink:GenomicEntity'],  # ✅ Valid
    'name': 'Test Gene'
}

Mixins like GenomicEntity, PhysicalEssence, and OntologyClass are now correctly recognized as valid categories.

Warning

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Original prompt

---

This section details on the original issue you should resolve

<issue_title>why is GenomicEntity not an allowed class for a node category?</issue_title>
<issue_description>Our team just ran our latest KGX knowledge graph through validate_biolink_kgx.py, and we are seeing warnings like this:

          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/247 has potentially invalid category 'biolink:GenomicEntity'",
            "instance_path": "unknown"
          },

On one level, I'm happy it's not an error, but on another level, I'd like to understand why. Is it because genomic entity is a mixin?

Thanks,
Steve</issue_description>

Comments on the Issue (you are @copilot in this section)

@saramsey Tagging @sierra-moxon @mbrush and @RichardBruskiewich @saramsey Also see this issue: https://github.com/biolink/biolink-model/issues/1405 @saramsey I know we allow edge predicates to be mixins, but maybe not node categories? @sierra-moxon I think this warning is invalid. It comes from the validator using BMT, which has flags for including or excluding mixins. Those flags aren’t being set in the validator, but they should be.

• Fixes why is GenomicEntity not an allowed class for a node category? #214

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[sierra-moxon]

This ended up being a bit more of a collaboration than a fully co-pilot, solved issue. tbf, I extended the scope a bit to centralize biolink naming convention transforms into a central method and reused bmt there.