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AIRR Community Data Standards
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collection_time_point_relative and units #587

Closed bcorrie closed 1 year ago

bcorrie commented 2 years ago

From a group that is trying to curate a data set - a question about collection_time_point_relative

Related to but not the same as #504

This group has a time series (subject sampled at multiple times), but doesn't actually have a duration between visits. So it isn't "day 1", "day 30", and "day 60", it is "visit 1", "visit 2", and "visit 3". The need is to group samples that are taken at specific "visits" (e.g. on "visit 2").

I think we want something like this:

collection_time_point_reference = 'subject enrollment'
collection_time_point_relative = 2
collection_time_point_relative_unit = 'visit'
collection_time_point_relative_unit_id = 'UO:????????' - an ontology ID that represents relative time.

It seems like it might be a common use case to require an ordinal scale for this data.

It seems like one way to represent this is:

collection_time_point_reference = 'subject enrollment'
collection_time_point_relative = 2

with no units?

bussec commented 2 years ago

How about the "count unit" (UO:0000189): "A dimensionless unit which denotes a simple count of things."?

bcorrie commented 2 years ago

Nice, I think that could work... Missed that branch of the tree...

scharch commented 1 year ago

@bcorrie ok to close?