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

[bclenet]

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

• BIDS specification changes
  - [ ] being proofread
• BIDS schema changes
  - [ ] validator error : /prov/* NOT_INCLUDED
  - [ ] validator error : /prov/*.json SIDECAR_WITHOUT_DATAFILE
  - [ ] validator error : derivative files are listed as NOT_INCLUDED / ALL_FILENAME_RULES_HAVE_ISSUES /FILENAME_MISMATCH / ENTITY_WITH_NO_LABEL
• BIDS examples
  • [BEP028] provenance - fMRIPrep preprocessing #502
  • [BEP028] provenance - SPM preprocessing #497
  • [BEP028] provenance - heudiconv conversion #496
  • [BEP028] provenance - dcm2niix conversion #494

[bclenet]

Hi @effigies ,

Here are quick questions about the schema modifications in this PR.
I tested the BIDS examples listed in the description of this PR against a BIDS validator using the modified schema, but I still encounter errors.

• Provenance files (.json) inside the prov directory are considered as sidecars, leading to SIDECAR_WITHOUT_DATAFILE error files
• Provenance files (.json) inside the prov directory are NOT_INCLUDED according to the validator, although

I think this is due to the fact that the src/schema/rules/files/common/modality_agnostic.yaml file I've added has no impact for now.

Also, files inside derivative datasets lead to NOT_INCLUDED / ALL_FILENAME_RULES_HAVE_ISSUES / FILENAME_MISMATCH / ENTITY_WITH_NO_LABEL errors because their names do not conform to BIDS naming. It seems to be contradictory to this part of the spec

Could you please give your thoughts about these ? Let me know if I should post these anywhere else.

Thanks,

[cmaumet]

@satra @yarikoptic: a point on which we'd love your input w/ @bclenet. It seems to us a bit problematic to use the word "Entity" in the Provenance spec for BIDS since entity in BIDS is already defined (and is different from the meaning we give in BIDS-Prov). We could easily use a different word (that would still be mapped to prov:Entity in the context file), but which word...

Just found out about "Transput" which seems to be a blanket term for both Inputs and Outputs, would that work for you both? Or any other suggestions?

Thanks!

[cmaumet]

Hi @bclenet !

Thanks for this version. I've included a number of comments (mainly some rephrasing).

[cmaumet]

Camille stopped her review here ----