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Example datasets for bep036 #465

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Arshitha
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@Arshitha Arshitha commented Aug 29, 2024

Added pheno001 and pheno002 example dataset inspired by ds004215 on OpenNeuro but significantly modified to keep it simple and easy to convey the various use cases proposed in BEP036.

Use cases covered (and to be added to this PR):

  • pheno001 - Single session with both phenotype and imaging data
  • pheno002 - Two sessions with one imaging data only session
  • pheno003 - Two sessions with one phenotype data only session
  • pheno004 - Two sets of sessions. One set of sessions (e.g. screening, baseline, followup, etc) for phenotype data and another set of sessions (e.g. 01, 02, etc) for imaging data.

Still in draft state but would appreciate any and all feedback.

Pinging co-contributors: @ericearl @SamGuay @surchs

@Arshitha Arshitha marked this pull request as draft August 29, 2024 21:20
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This is great, thanks! I'm guessing you left it in draft state becausew of pheno001 and pheno002, right?

I think we should remove the age_at_visit column/field from all phenotype/ measurement tools and instead provide a root-level sessions file with that field. Should we maybe take that a step farther and RECOMMEND or say it's OPTIONAL to add age to the sessions file?

@Arshitha
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I like that idea. It's redundant information that can be aggregated to sessions level, and can be a recommendation in the BEP.

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It's in Draft state because I haven't prepared pheno003 and pheno004 but yes, all four example datasets will violate the contribution guidelines.

"f": "Female"
}
},
"age_at_visit": {

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Suggested change
"age_at_visit": {
"age": {

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In this case, age_at_visit would be the same as age and that's the reason I changed it to age_at_visit.

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I think it's still fine to keep as age, but I would let @SamGuay and/or @surchs be the tie-breakers.

@@ -0,0 +1,3 @@
participant_id sex age_at_visit MRI ace demographics

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Suggested change
participant_id sex age_at_visit MRI ace demographics
participant_id sex age MRI ace demographics

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same as previous comment

pheno002/sessions.json Outdated Show resolved Hide resolved
pheno002/sessions.tsv Outdated Show resolved Hide resolved
pheno003/sessions.json Outdated Show resolved Hide resolved
pheno003/sessions.tsv Outdated Show resolved Hide resolved
Arshitha and others added 4 commits August 30, 2024 15:59
Co-authored-by: Eric Earl <eric.earl@nih.gov>
Co-authored-by: Eric Earl <eric.earl@nih.gov>
Co-authored-by: Eric Earl <eric.earl@nih.gov>
Co-authored-by: Eric Earl <eric.earl@nih.gov>
@christinerogers
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christinerogers commented Oct 24, 2024

Got a question from @dominikwelke --

Could this PR include an example showing how to represent multiple runs from one participant-session?

@ericearl mentioned today this is easily done by adding a run column in the .tsv, would be nice to see illustrated and mentioned here.

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3 participants