[ENH][BEP028] Specification update for BEP028 BIDS-Prov

[bclenet]

This is a work in progress PR proposing a specification update for BEP028 BIDS-Prov.

Todo lists

• Road to community review - Top priorities BEP028_BIDSprov#167
• Road to community review - Secondary priorities BEP028_BIDSprov#168

Blocking points

• [schema] allow for an optional subdirectory prov/[prov-<label>] BEP028_BIDSprov#169
• [schema/validator] different usages of GeneratedBy BEP028_BIDSprov#170
• [ci] pdf rendering error due to "multiline links" BEP028_BIDSprov#171
• [validator] provenance files are considered as sidecars BEP028_BIDSprov#172

Associated BIDS examples

• [BEP028] provenance - study dataset + manual annotation #519
• [BEP028] provenance - fMRIPrep preprocessing #502
• [BEP028] provenance - SPM preprocessing #497
• [BEP028] provenance - heudiconv conversion #496
• [BEP028] provenance - dcm2niix conversion #494

[bclenet]

Hi @rwblair,
Thanks for the comment and review.

Most of the rules you propose are related to the validation of the provenance metadata itself. I believe that these could be brought later to the validator / schema ? I agree that this is easier to validate once the metadata is aggregated; I understood you found the python code to do that. I also plan to write python code for defects detection in a provenance graph (e.g.: isolated nodes, undefined objects, etc.) which could later help for validation.

About Ids, we need to be more precise in the specification about that. The idea is that we want to have BIDS URIs as much as possible, also because it's more human readable. But at the same time, we want to ensure uniqueness of the Id outside the dataset, which is not the case for BIDS URIs as currently defined.

Does it make sense to you ?

[cmaumet]

@bclenet While thinking about the first two points on how to validate certain parts of the files I started to realize the nature of the changes that will be required of the schema to validate them.

@rwblair thanks a lot for this detailed overview. I second @bclenet's comment in that we were thinking of a much lighter validation using the BIDS schema (mainly making sure that the newly created files had a proper naming and that the keys inside the metadata files corresponded to what is in the spec). I was hoping we could focus on this first before we open the BEP for community review.

@rwblair @effigies: Could we plan a quick meeting to identify the remaining steps we need to follow in order to update the schema for BIDS-Prov (BEP028)? So we can have a clearer plan of when we'll be able to open for community review. Thank you!