Add collection device and collection method metadata fields to all packages

[AmandaBirmingham]

This suggestion is from Alan Jarmusch in the Dorrestein lab, via email:

a few things that I think the end user will appreciate: .... .... iii) add a metadata column to all packages in which the collection device & collection method are defined. For example, urine package: collection device ("sterile plastic collection container, manufacturer BD #serial number, lot#") & collection method ("clean catch")

the last one (iii) has been problematic for the metabolomics side (sequencing is likely to be more immune)- samples provided in multiple types of tubes (or swabs from different lots/years) with different reagents which ultimately lead to separation based on that information. tracking this information will at least allow us to go back and understand potential sources of the variance observed.

[AmandaBirmingham]

Austin provided this comment on the suggestion, via email:

Amanda this might be one of those cases where we'd ideally like to have standard options based on the list of kits we recommend, but also the ability for users to add others so let's add this to the list to discuss before implementing.

[adswafford]

For the beta release, let's enforce these columns being present for all studies but not controlled vocabulary for now.

[AmandaBirmingham]

@adswafford @stephanieorch If they really need to be included for every (microbiome) study, they should be added to the EBI-submittable package in ebi-submittable.xlsx . I'm tagging Stephanie to do this one unless someone tells me otherwise :)

[adswafford]

Pinging @stephanieorch to close if complete. Also need to add 'tube_id' to ebi-submittable.xlsx

[stephanieorch]

fixed in the recent pull request