what does '... or culture independent'. mean in terms of the `Expected value` from 'culture target microbial analyte'?

[ramonawalls]

@turbomam Which package and term is this referring to?

[only1chunts]

This is the term Mark is referring to:

Term name - culture target microbial analyte Structured comment name - cult_target Definition - The target microbial analyte in terms of investigation scope. This field accepts terms under organism (http://purl.obolibrary.org/obo/NCIT_C14250). This field also accepts identification numbers from NCBI under https://www.ncbi.nlm.nih.gov/taxonomy. Expected value - NCIT:C14250 or NCBI taxid or culture independent Value syntax - {termLabel} {[termID]}|{integer} Example - Listeria monocytogenes [NCIT:C86502] Term ID - MIXS:0001119 Package(s) - Food

The Expected value includes "or culture indendent"

[lschriml]

If the analyze is in NCBI, the NCBI taxis is to be reported, or the name of the organism from NCIT:C14250, https://www.ebi.ac.uk/ols/ontologies/ncit/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FNCIT_C14250 or to it is to be noted that the 'analyze' is 'culture independent'

[turbomam]

Thanks, @lschriml. Maybe I still don't understand, but I'm sure we can get this to a good place tomorrow.

Are you saying that the Expected values for 'culture target microbial analyte' include all of the following:

• a numerical NCBI taxon identifier
• a subclass of NCIT:C14250
• the static text "culture independent"

If that really is the case, then the Value syntax will need to be changed, because right now it only allows for an ontology term (in a prescribed format) or an integer.

That seems like a lot of entirely different patterns that should be allowed for one filed. Do we really aspire to provide validation support for it?

[lschriml]

Hello Mark, yes, the Expected value can be one of the three. NCIT:C14250 or NCBI taxid or culture independent

Value Syntax: {termLabel}|{[termID]}|{integer}|[culture independent]

These are the options for the types of expected data for the field.

Cheers, Lynn