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[ENH] Schema changes related to BEP032 #1826

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@ree-gupta ree-gupta commented May 17, 2024

  • BIDS BEP032 Proposal
  • Contributes to [ENH] microelectrode electrophysiology specification (BEP032) #1705
  • Related issue about age Formalize participants' age to clarify the reference point #1634
  • Clarify if columns can have arrays as value, if not, how do we handle the surgery_date
  • Add columns for _probes.tsv
  • Add tabular_data rules for _probes.tsv
  • Add columns for _electrodes.tsv
  • Add tabular_data rules for _electrodes.tsv
  • Add columns for _channels.tsv
  • Add tabular_data rules for _channels.tsv
  • Add columns for _scans.tsv
  • Add tabular_data rules for _scans.tsv
  • Add columns for _events.tsv
  • Add tabular_data rules for _events.tsv
  • Add sidecars rule for _coordsystem.json
  • Add sidecars rule for _ephys.json
  • Fix language conventions, such as for e.g. -> for example,
  • Discuss and clear TODOs commented out in the schema
  • Add file naming and other modality-specific rules
  • Fix schema validation errors

@bids-standard/bep032

@ree-gupta ree-gupta changed the title [ENH] Schema changes related to particiapants.tsv for BEP032 [ENH] Schema changes related to participants.tsv for BEP032 May 17, 2024
@ree-gupta ree-gupta marked this pull request as ready for review May 17, 2024 11:03
enum:
- $ref: objects.enums.postnatal.value
- $ref: objects.enums.fetal.value
- $ref: objects.enums.gestational.value
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Thank you @ree-gupta ! I wonder if we better propose this as a PR against current bids version, just keep surgery_date for the BEP032 but propose age_category and age_type .

It also would complement

Then it would give it a better chance for discussion etc.

Also I guess they should be added as recommended to
https://github.com/bids-standard/bids-specification/blob/master/src/schema/rules/tabular_data/modality_agnostic.yaml#L2

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Done! Also, birthdate is another column suggested by the BEP032.

Comment on lines 1419 to 1421
Also known as "embryonic age," this measures the age of a
fetus or embryo from the time of conception. It's typically about two weeks
less than the gestational age.
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For humans, but not other species, right? Or is this common across a broad spectrum of species?

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I am not sure. For now, I removed these changes from here as suggested by Yarik and moved them to #1839 where it reflects the bep032 doc in its current state.

@ree-gupta ree-gupta changed the title [ENH] Schema changes related to participants.tsv for BEP032 [ENH] Schema changes related to BEP032 May 27, 2024
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3 participants