microbiomedata / nmdc-schema

National Microbiome Data Collaborative (NMDC) unified data model
https://microbiomedata.github.io/nmdc-schema/
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work on enum and permissible value names/texts #931

Closed turbomam closed 8 months ago

turbomam commented 1 year ago
Shalsh23 commented 1 year ago

Adding more context given by @turbomam in slack discussion:

This concerns enums in all YAML files in src/schema, including src/schema/portal, but not including src/schema/mixs.yaml.

  1. According to https://linkml.io/linkml/schemas/linter.html#standard-naming, the names/keys of the enums should be PascalCase/UpperCamelCase. YesNoEnum in src/schema/nmdc.yaml meets that standard, but the nearby biosample_category_enum doesn’t.
  2. We should also to look for opportunities to consolidate enums with the same or virtually identical permissible_values . That requires a little more creativity or discretion. If you do find two enums with essentially the same permissible_values, then you could look for slots that use the to-be-deprecated enum in their range and switch it to the to-be-retained enum. The delete the definition of the to-be-deprecated enum.
  3. If you pursue the second task above, you may see that there are lots of opportunities for consolidating enums in mixs.yaml, but I and a few other people from the Genomics Standards Consortium are working on totally regenerating the MIxS schema.