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EBISPOT / gwasdepo-deposition-service

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Extend the study template to capture Study Flag attributes during upload #151

Closed sprintell closed 2 years ago

sprintell commented 2 years ago

Extend the study template feature to capture Study Flag attributes during upload

ala-ebi commented 2 years ago

*add 3 columns 'Sumstats', 'GxE' and 'Pooled' --- on header give description of each flag each column would be preferred to be YES/NO a dropdown on the template

*on DB they should be study level boolean attributes

*display the values in the study UI

ala-ebi commented 2 years ago

@ljwh2 need to add descriptions for the 3 flags in the template: 'Sumstats', 'GxE' and 'Pooled' can you suggest descriptions for them please?

ljwh2 commented 2 years ago

Sumstats: Enter yes if summary statistics are available for this study GxE: Enter yes if the study is a GxE interaction analysis Pooled: Enter yes if the study design uses pooled DNA from multiple individuals

ljwh2 commented 2 years ago

Just a note that it should be efficient for the curator to enter flags of a publication (considering many studies per publication). So dropdown may not be the best approach if it necessitates a separate click per study (compared to copying down the text)

ala-ebi commented 2 years ago

@ljwh2 thanks.

to enter flags of a publication

did you mean flags for studies of a publication? because that's what I thought we're doing here.

also should those fields be mandatory?

and for which templates? empty metadata, curator empty metadata, curator prefilled metadata, ss, curator ss?

ljwh2 commented 2 years ago

did you mean flags for studies of a publication? because that's what I thought we're doing here

Yes, sorry

ljwh2 commented 2 years ago

I will discuss the questions with curators and get back to you

ljwh2 commented 2 years ago

For the templates, the fields do not need adding to ss, curator ss. 'GxE' and 'Pooled' should be in empty metadata, curator empty metadata "Sumstats" should only be in curator empty metadata

The fields should not be mandatory. If no value is entered, the default value in the DB should be "no"

ljwh2 commented 2 years ago

As discussed, the Sumstats flag should be a new management field for curators to use for prioritisation only. It should be populated with yes if the submission has sumstats, or also can be set manually. This field will not be represented in the curation DB. Curators currently get data from the curation DB for prioritisation, so will need to find a workaround during this interim time.

ljwh2 commented 2 years ago

@ala-ebi see comments above