collection_date

[mslarae13]

Current term details Please supply the current details of the term that you would like to update:

Term name - collection_date
Term ID - [if known]
Structured comment name - 
Definition -  Date sample was collected
Expected value -  date
Value syntax -
Example -
Preferred unit - yyyy-mm-ddTHH:MM:SS
Package(s) - all

Suggested update(s) Please supply the new suggestions for any of the details listed below (only insert text to those details that should be updated):

Term name - 
Structured comment name - 
Definition - 
Expected value - 
Value syntax -
Example -
Preferred unit - 
Package(s) - 

Additional context Specifically within soil or sediment, often in a lab incubation, material is collected from the field, brought back to the lab & an incubation with treatments is performed. Often years later. For example, soil collected in 2014, and later a lab incubation is done with plant growth and temperature treatments. There's not a good way to separate field collection date and incubation collection date. Parent -> child relationships can link this. But doesn't explicitly define.

Add any other context about the update request here, e.g. why you think this needs to be updated.

[mslarae13]

@wdduncan

@cmungall

[mslarae13]

NMDC is adding incubation start and collection date

[only1chunts]

If a submitter asked me how to represent your scenario I think I would suggest the GSC term MIXS:0000016: Term name: sample material processing Definition: Any processing applied to the sample during or after retrieving the sample from environment. This field accepts OBI, for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI

Are you asking us to look at updating the collection date term here? If so, please can you specify what the change you're proposing is? If not, can I close this ticket? Thanks.

[mslarae13]

@only1chunts

With a quick search on OBI (I'd say a bit longer than I would expect someone filling out metadata to spend), I don't see a term that well details a lab incubation. Also, even if I can add a lab incubation date, I can't add a start & harvest date. Now, one could argue, that by providing a source material or parent-child sample link, you'd have the field collection date from the "parent material", and the collection date of the 'new' sample (the lab incubation sample) would be the date the incubation ended. However, that leaves a lot of room for missed information. When a soil, sediment, or plant is harvest from the field, say October, is VERY different carbon chemistry than in say June. If someone harvests soil from the field then does a lab incubation 6 months later, the collection date can be misleading.

I think the term Collection Date should be updated / clarified for exactly at what point the sample is being collected (field vs lab/experiment end). As well as the addition of new terms. Say if a lab incubation is performed, indicate that in sample material processing (if non OBI terms can be used in this field?/ if there's a term in OBI that indicates this) & then provide the start and stop dates (lab_inc_start/end term addition).