microbiomedata / mixs-6-2-release-candidate

Proposed, Harmonized MIxS 6.2
https://github.com/GenomicsStandardsConsortium/mixs6.2_release_candidate
MIT License
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Do we want slots like `farm_equip` to be validated against the term label/term id syntax, or the AGRO:00000416 parent class? #172

Open turbomam opened 1 year ago

turbomam commented 1 year ago

see also

turbomam commented 1 year ago

For example, config/linkml-stage-mixs-modifications.yaml can assert that slot farm_equip has range of FARM_EQUIP_ENUM, which can be defined as

  FARM_EQUIP_ENUM:
    reachable_from:
      source_ontology: obo:agro
      source_nodes:
        - AGRO:00000416
      relationship_types:
        - rdfs:subClassOf
      is_direct: False
      include_self: False
      traverse_up: False

then, using the prototype vskit command in project.Makefile, FARM_EQUIP_ENUM will have the class IDs of subclasses of AGRO:00000416 assigned as permissible_values.

At that point, AGRO:00000676 would be an acceptable value for farm_equip, but values in the traditional pattern like "feed pan [AGRO:00000676]" wouldn't be

turbomam commented 1 year ago

see also