Add additional case associations to represent phenopackets

[kevinschaper]

Draft PR with @iQuxLE to represent phenopackets in biolink for Monarch KG

• case to disease
• case to variant
• case to gene
• biological sex property for case entity
• add phenopacket-store infores ID if it doesn't already exist: https://github.com/biolink/information-resource-registry

[Copilot]

Pull Request Overview

This PR introduces additional association types and properties to support phenopacket representation in the Monarch KG biolink model. Key changes include:

• New association classes for case to disease, case to variant, and case to gene.
• Addition of a biological sex slot and new qualifiers mixins.
• Updates to slot definitions and mixins for consistency across association definitions.

Reviewed Changes

Copilot reviewed 2 out of 2 changed files in this pull request and generated 1 comment.

File	Description
src/biolink_model/schema/biolink_model.yaml	Adds new case association classes with explicit subject, predicate, and object slots
biolink-model.yaml	Introduces the "has biological sex" slot and new association definitions with adjusted slot usage and mixin updates

Comments suppressed due to low confidence (1)

biolink-model.yaml:10834

• Confirm that the removal of the 'entity to disease association mixin' from the 'behavior to behavioral feature association' block is intentional and consistent with the overall association design.

-      - entity to disease association mixin

[kevinschaper]

This is odd, the check dependencies job is installing linkml 1.9.1, but the poetry.lock is still at 1.8.7.

[sierra-moxon]

should subject be restricted with range: case ?

[iQuxLE]

This is already described in case to entity association mixin so it should be fine

[sierra-moxon]

can you give me a short description in this PR on why mixins are needed here?

[iQuxLE]

I used mixins to follow the established pattern seen in case to phenotypic feature association -> entity to phenotypic feature association mixin -> entity to feature or disease qualifiers mixin to ensure consistent semantics across the new case associations.

This keeps the pattern consistent throughout the model while improving readability by avoiding duplication and keeping the focus on the core purpose of each new association type.