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`heavy_metals` description and guidance is not LinkML compliant

Open mslarae13 opened this issue 1 year ago • 1 comments

https://genomicsstandardsconsortium.github.io/mixs/0000652/

Current:

heavy_metals:
    annotations:
      Expected_value: heavy metal name;measurement value unit
      Preferred_unit: microgram per gram
    description: Heavy metals present in the sequenced sample and their concentrations.
      For multiple heavy metals and concentrations, add multiple copies of this field

Description's guidance, "For multiple heavy metals and concentrations, add multiple copies of this field" You can't do this in LinkML & this guidance won't validation. Rather, it should be a compound field separated by a ; or | (See https://github.com/GenomicsStandardsConsortium/mixs/issues/465#issuecomment-2256412091)

so ...

examples:
    - value: mercury;0.09 micrograms per gram

Change to

examples:
    - value: mercury,0.09 micrograms per gram
    - value: mercury,0.09 micrograms per gram | lead,0.05 micrograms per gra,

mslarae13 avatar Sep 19 '24 23:09 mslarae13

i agree with this, but we should review our exceptions about using whitespace between the pipe delimiter and the values on either side. I think that the following example

"mercury,0.09 micrograms per gram | lead,0.05 micrograms per gram"

would be expanded to these by most software applications

  • "mercury,0.09 micrograms per gram "
  • " lead,0.05 micrograms per gram"

So I would have written the example as "mercury,0.09 micrograms per gram|lead,0.05 micrograms per gram"

turbomam avatar Sep 24 '24 16:09 turbomam