Create and then store Neurobagel data dictionaries from bulk annotation

[surchs]

Given an annotated file (e.g. spreadsheet) from https://github.com/neurobagel/bulk_annotations/issues/2, I want to run a process so that I get a Neurobagel .json data dictionary for each dataset annotated in the bulk file. I then also want to store these .json files in a place where they are easily accessible and reused.

• [x] Create a prototype for 3 datasets that turns the annotated .tsv into Neurobagel .json

• [x] Ensure that the .json files we create have

  • [x] everything that was in the original, user supplied .json (i.e. nothing is lost)
  • [x] everything we have annotated
  • [x] comply with our schema
• [x] Refactor the prototype to something we can reuse more than once if needed
• [x] Add tests (I need them...)
• [x] Make sure IsPartOf is processed for assessment tools
• [x] Run the .tsv to .json thing on all the datasets we have annotated

[surchs]

See https://github.com/con/job/issues/1#issuecomment-1556231092

[surchs]

Blocked by #2

[surchs]

Unblocked by https://github.com/neurobagel/bulk_annotations/issues/10

[surchs]

That was premature... Blocked by my availability. Will get to #2 first, then to this

[surchs]

Unblocked because #2 is done/under review

[surchs]

Slight change of plans: the outputs of this work should now go and live under https://github.com/neurobagel/openneuro-annotations