Normalize inconsistencies in term MIXS:0000002

[turbomam]

One example of the broader issue #438

Here's an analysis of ["Definition", "Occurrence", "Package item", "Structured comment name", "Value syntax"] values for MIXS:0000002. If there's no entry for one of those fields (like "Occurrence"), it means that it was used consistently across "Environmental package"s

Definition:
  agriculture: The device used to collect an environmental sample. This field accepts
    terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO).
    This field also accepts terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094).
  food-animal and animal feed: The device used to collect an environmental sample.
    This field accepts terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO).
    This field also accepts terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094).
  food-farm environment: The device used to collect an environmental sample. This
    field accepts terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO).
    This field also accepts terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094).
  food-food production facility: The device employed for collecting the sample.
  food-human foods: The device used to collect an environmental sample. This field
    accepts terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO).
    This field also accepts terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094).
Package item:
  agriculture: sample collection device or method
  food-animal and animal feed: sample collection device
  food-farm environment: sample collection device
  food-food production facility: sample collection device
  food-human foods: sample collection device
Value syntax:
  agriculture: '{text}'
  food-animal and animal feed: '{termLabel} {[termID]}|{text}'
  food-farm environment: '{termLabel} {[termID]}|{text}'
  food-food production facility: '{text}'
  food-human foods: '{termLabel} {[termID]}|{text}'

The only match for "sample collection device" at https://www.ncbi.nlm.nih.gov/biosample/docs/attributes/ is

Name	Harmonized name	Synonyms	Description	Format
sample collection device or method	samp_collect_device	samp collect device,sampling device	Method or device employed for collecting sample	{text}

I propose that

• all of the Package items be normalized to 'sample collection device or method'
• all of the Value syntaxes be normalized to '{text}'

I'm less certain about how we should handle the Definitions. NMDC's value of "Method or device employed for collecting sample" sure seems like a good definition.

If we switch to using schemasheets #439, then some of the variations in the Definitions (which LinkML models as descriptions) could be put into comments, notes or todos (at the risk of the template getting wider).

[lschriml]

In MIxS 6.0, we split the older mixs term: sample collection device or method into two terms.

to edit, to standardize structure comment name, across packages:

--> update the Structured comment name agriculture samp_collect_method food-animal and animal feed samp_collect_method food-food production facility samp_collect_method food-human foods sample_collec_method

--> update the agriculture Package Item name: agriculture samp_collect_device sample collection device or method

food-animal and animal feed samp_collect_device sample collection device