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[ENH] Add phenotype and rawdata directories to "study" datasets #2191

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[ENH] Add phenotype and rawdata directories to "study" datasets #2191

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b99a7bd
Suggested modifications to directory layout of the bids-study Dataset…
nikhil153 Sep 2, 2025
2d59198
fixed minor typos
nikhil153 Sep 2, 2025
7fc71c7
Merge branch 'bids-standard:master' into master
nikhil153 Sep 9, 2025
e0fe3ce
removed bids prefix from the DatasetType and subdirs.
nikhil153 Sep 10, 2025
924d1c5
Merge branch 'master' into master
nikhil153 Oct 29, 2025
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22 changes: 16 additions & 6 deletions src/schema/rules/directories.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -16,14 +16,16 @@
# The special "root" specifier describes the root of the dataset and only defines subdirectories.
# No naming convention applies, and the requirement level and opacity would be superfluous.
#
study:
bids-study:
root:
subdirs:
- code
- docs
- derivatives
- bids-raw
- bids-derivatives
- logs
- sourcedata
- phenotype
code:
name: code
level: optional
Expand All @@ -32,8 +34,12 @@ study:
name: docs
level: optional
opaque: true
derivatives:
name: derivatives
bids-raw:
name: bids-raw
level: optional
opaque: true
bids-derivatives:
name: bids-derivatives
level: optional
opaque: true
logs:
Expand All @@ -44,8 +50,12 @@ study:
name: sourcedata
level: optional
opaque: true
phenotype:
name: phenotype
level: optional
opaque: false
Comment on lines +53 to +56
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@effigies effigies Sep 4, 2025

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This was removed after this discussion: #2185 (comment)

I didn't see a justification for re-adding it, so I want to make sure this isn't slipped in with little consideration.

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@nikhil153 nikhil153 Sep 10, 2025

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Yes, should have explained this addition based on offline conversations.
The reason for removing phenotype directory was that it would presumably appear in the raw dataset. But isn't that true for derivatives directory as well? It's a bit confusing having derivatives part of all three DatasetTypes but enforcing phenotype only be part of raw or derivative. In practice, phenotype data curation is likely to be more independent than that of derivatives, which is one of the reasons we prefer it to be at the top level.

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@effigies effigies Jan 16, 2026

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Sorry for the long silence.

The reason for removing phenotype directory was that it would presumably appear in the raw dataset. But isn't that true for derivatives directory as well? It's a bit confusing having derivatives part of all three DatasetTypes but enforcing phenotype only be part of raw or derivative. In practice, phenotype data curation is likely to be more independent than that of derivatives, which is one of the reasons we prefer it to be at the top level.

So the logic in derivatives is that any raw dataset is a valid derivative dataset, so you cannot restrict, you can only expand. Furthermore, you can have derivatives of derivatives, so nesting is entirely reasonable. I suppose you could preprocess phenotypic data and include it in a derivative, so it might even make sense.

IMO, if phenotypic data is worth including in the study, it's worth including in the raw data, regardless of the independence of curation. I still don't see the use case for phenotype at the study level.

That said, I won't block this.


raw:
bids-raw:
root:
subdirs:
- code
Expand Down Expand Up @@ -103,7 +113,7 @@ raw:
level: required
opaque: false

derivative:
bids-derivative:
root:
subdirs:
- code
Expand Down
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