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Followup on #353 - support including annotations in schemas to model KGX output #356

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caufieldjh opened this issue Mar 26, 2024 · 1 comment

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@caufieldjh
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Schemas may currently be annotated with the owl slot to denote the OWL equivalent, e.g., in the recipe schema:

  FoodItem:
    is_a: CompoundExpression
    annotations:
      owl: IntersectionOf
    attributes:
      food:
        description: the food item
        range: FoodType
        slot_uri: BFO:0000051
        annotations:
          owl: ObjectProperty, ObjectSomeValuesFrom
      state:
        description: the state of the food item (e.g. chopped, diced)
        annotations:
          owl: DataProperty, DataHasValue

This only comes into play when serializing as OWL.

We can do the same for KGX, as the schema does not define whether a class defines a node, edge, higher-level association, etc.
The annotations field should be able to accept explicit directions for what should be subject, predicate, object and properties.

Perhaps this should be present elsewhere in the LinkML infrastructure.

@caufieldjh
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At BBOP group meeting today @cmungall mentioned there is general undocumented support in LinkML to handle these kind of annotations but they aren't generally processed by any utility. Would be useful to have a similar strategy for KGX, such that it is treated as a "flavor" of CSV with some added considerations.

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