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microbiomedata / nmdc-schema

National Microbiome Data Collaborative (NMDC) unified data model
https://microbiomedata.github.io/nmdc-schema/
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has unit appears as a slot for Biosample #1723

Closed turbomam closed 8 months ago

turbomam commented 9 months ago

look at all of these slots with spaces in their names in Biosample!

      - has numeric value
      - has raw value
      - has unit

the search in the online documentation doesn't make it easy to see that there are has_unit and has unit slots or which classes use them.

turbomam commented 9 months ago

poetry run linkml-lint --format tsv --output nmdc.yaml.lint.tsv src/schema/nmdc.yaml does not catch those slots with whitespace in their names.

PS we could have a TSV liniting target in project.Makefile in addition to the basic one in Makefile

turbomam commented 9 months ago

see also

turbomam commented 9 months ago

@sujaypatil96 observed that it also appears in mixs.yaml

I think that once the slot assignment is deleted from Biosample, its presence in mixs.yaml won't re-inject the assignment back into Biosample.

But removing it form mixs.yaml is preferable. Having said that, we will be switching to importing from GSC's mixs.yaml (v6.2.0) soon, replacing our current practice of importing from our static mixs.yaml.

turbomam commented 9 months ago