Description
Quite often projects do not adopt BIDS due to complexity or not perfect fit, and then establish new a file layout and/or metadata convention/standard while saying they are "BIDS-like". The likeness varies greatly. Quite often it is simply the aspect of having folders and file names with some metadata in them. Those are not worth mentioning here. But there is a good number of BIDS-like standards (in my words - formalized descriptions adopted by a considerable number of people) which are worth reviewing and analyzing for what could minimize divergence between them and current BIDS through possibly introducing missing but reasonable and desired features into BIDS 2.0.
This issue would be used to collect pointers and possibly summarize rationale and major features behind them.
DANDI layout
Established by me and @satra for https://dandiarchive.org, primarily due to complete lack of usable standard/layout at that earlier point in time .
- There is no specification, and layout is largely "enforced" via
dandi organizecommand on a set of .nwb files. dandiset.yamlschema is defined within pydantic model in https://github.com/dandi/dandi-schema/blob/master/dandischema/models.py#L1405- see Convergence between DANDI Layout and BIDS dandi/dandi-cli#1498
Notable divergences:
- no
dataset_description.json- metadata is in "in-house"dandiset.yaml - no
ses-*/level subfolder but there isses-entity in the target filenames (convergence possible through Make it possible to specify folders layout to be other than sub-{label}/[ses-{label}/] #54) - no datatype (AKA modality) subfolder (related: Change modality directories to entity format #55, convergence possible through Make it possible to specify folders layout to be other than sub-{label}/[ses-{label}/] #54)
- main file format is
.nwb(convergence through https://bids.neuroimaging.io/bep032 for animal ephys data, discussed/not (yet) accepted in BIDS 1.0 formicr/: Allow for .nwb standard/file format to be used for "micr" bids-specification#1632) - entity labels/values could contain
-and+. (TODO: ref BIDS PR) - Suffix can contain
+(no PR yet I think) - Suffix contains (often multiple) data modalities contained within the single .nwb file, concatenated with
+
PsychDS
https://psych-ds.github.io/ https://github.com/psych-ds/psych-DS (attn @mekline and @bleonar5 - would appreciate details/feedback alike for DANDI here or in a dedicated issue/doc)
- Overall motivation: Re-use BIDS schema formalization to derive a customized subset of the BIDS standard to simplify domain specific use and adoption.
NeuroBlueprint
https://neuroblueprint.neuroinformatics.dev/specification.html .
Request for summarization of rationale/divergences: neuroinformatics-unit/NeuroBlueprint#51
SPARC Data Structure (SDS)
The SPARC platform has a preprint online that describes a BIDS inspired data structure: https://www.biorxiv.org/content/10.1101/2021.02.10.430563v2. Rough details are also on their wiki.
TemplateFlow
https://www.templateflow.org/usage/archive/#acceptable-data-types
- A related discussion "has happened" in BEP Proposal: Atlas specification bids-specification#1281
Brain-Development.org Atlas
https://brain-development.org/brain-atlases/atlases-from-the-dhcp-project/cortical-surface-template/ describes itself as "using BIDS conventions", and proceeds to define custom entities and metadata.
NiPoppy
Study-level description which includes bids dataset and uses some conventions (like derivatives/ subfolder with clearer defined naming convention).
- Add DatasetType="project" and rework existing "layout" example into a proper BIDS dataset bids-specification#1861 attempts to converge NiPoppy and BIDS