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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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Expected value of food_product_type #165

Open ramonawalls opened 1 year ago

ramonawalls commented 1 year ago

In reviewing mixs_table_stage modifications, I see that your suggestion for the expected value of food_product_type is FOODON:00001002 or FOODON:03309997. Does this mean that it should be FOODON:00001002 or FOODON:03309997 or one of their subclasses? If so, it needs to be phrased more clearly.

turbomam commented 1 year ago

I agree, but this Expected value comes directly from the MIxS excel sheets.

LinkML allows the range for a slot like food_product_type to be set to an enumeration that has a reachable_from relationship with a ReachabilityQuery. If we use that, then the LinkML validator can check if the values provided in food_product_type (etc.) really come from subclasses of either FOODON:00001002 or FOODON:03309997.

BUT, the acceptable values will just be the ontology ids, not the "{term_label} [{term_id}]" pattern.

See also

ramonawalls commented 1 year ago

Okay, then we can leave it as is for now, but we should address this as a more general issue some day.