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GenomicsStandardsConsortium / mixs

Minimum Information about any (X) Sequence” (MIxS) specification
https://w3id.org/mixs
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negative control type [MIXS:0001321] #199

Closed only1chunts closed 3 years ago

only1chunts commented 3 years ago

New term details

Term name - negative control type
Term ID - MIXS:0001321
Structured comment name - neg_cont_type
Definition - Type of negative control.
Expected value - enumeration or text
Value syntax - [collection device control|collection tube control|DNA extraction blank control|PCR amplification control|swab control|syringe control] or {text}
Example -
Package(s) - negative control

Additional context Add any other context about the new term here.

pbuttigieg commented 3 years ago

Related to #200 too.

This field seems to focus on the stage of a workflow or a bit of apparatus, while the positive one [clarified in today's CIG call, the definition is not clear] is expecting the name of the positive control used (if from a company) or some sort of textual description.

It would be wise to align the value types expected by these fields, and to clarify the definitions in both. Right now this risks some difficulties downstream.

Enumeration here may not be the best way, as the values are unbounded. Like the positive control field, I'd simply have this as textual, but leave some examples as indicated.

I'd go more for:

Term name - negative control type
Term ID - MIXS:0001321
Structured comment name - neg_cont_type
Definition - The substance or equipment used as a negative control in an investigation.
Expected value - text
Value syntax - {text}
Example - [distilled water|phosphate buffer|empty collection device|empty collection tube|DNA-free PCR mix|sterile swab |sterile syringe]
Package(s) - negative control
ramonawalls commented 3 years ago

I agree with @pbuttigieg 's proposal, but change value syntax to term or text so it matches positive control

we need confirmation from @josieburgin.

only1chunts commented 3 years ago

I have added the term with details below to the v6 CORE and set to "C" conditional mandatory for all checklists, with an occurence of "1".

Structured comment name - neg_cont_type 
Term name - negative control type
Definition - The substance or equipment used as a negative control in an investigation.
Expected value - enumeration or text    
Value syntax - [distilled water|phosphate buffer|empty collection device|empty collection tube|DNA-free PCR mix|sterile swab |sterile syringe] or {text}
Term ID - MIXS:0001321

IF there are any changes requried to the above details please REOPEN this ticket (and tag me).

Term added to v6 spreadsheet and added to the change log