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Manage custom enumerations / vocabs #60

Description

@RobertJCarroll

We have some enumerations defined in the model with purely custom codes, eg, EnumDataCategory. We need to establish a workflow for these terms that may include creating an ontology so that we can support curies for all of our codes. That will also enable us to manage these terms a little bit separately from the model itself and leverage the work we are doing with term expansions.

  • Create a "temporary" ontology solution, perhaps with a basic yaml spec, that can hold our "known custom concepts that don't have mappings"
  • Update all enums to use the curies from the meaning as the values
  • Update CAM to support the expanded/explicit enums

Update all enums and fix the "null enumeration inheritance" issue (perhaps "inherits": https://linkml.io/linkml/schemas/enums.html)

Manual review and clean up steps:

  • Add Null Enumeration to fields where nulls are acceptable (as the enum inheritance options were deemed less desirable)
  • Review existing enums that do not have meanings and find standard terms where possible
  • Update any concept-centric fields that are just uriorcurie as Concept type- this will support us understanding gaps in our concept coverage when people put uriorcuries in we "don't understand"
  • Add any-of Enums for our "recommended" or "example" type bindings, eg, for Program names. This allows broad use of fields, but gives our harmonizers context.

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