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[ENH] Add stimulus and annotation entities #1814

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[ENH] Add stimulus and annotation entities #1814

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51fee52
Add stimulus and annotation entities
neuromechanist May 6, 2024
cee0301
Add stim_id field to columns.yaml
neuromechanist May 6, 2024
2bc513d
Correct typo in entities.yaml
neuromechanist Aug 6, 2024
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8 changes: 8 additions & 0 deletions src/schema/objects/columns.yaml
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Expand Up @@ -603,6 +603,14 @@ stim_file:
For example `images/cat03.jpg` will be translated to `/stimuli/images/cat03.jpg`.
type: string
format: stimuli_relative
stim_id:
name: stim_id
display_name: Stimulus ID
description: |
A stimulus identifier of the form `stim-<label>`,
matching a stimulus entity found in `stimuli/` directory.
type: string
pattern: ^stim-[0-9a-zA-Z]+$
strain:
name: strain
display_name: Strain
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19 changes: 19 additions & 0 deletions src/schema/objects/entities.yaml
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Expand Up @@ -422,3 +422,22 @@ tracksys:
may be longer and more human readable.
type: string
format: label
stimulus:
name: stim
display_name: Stimulus
description: |
The `stim-<label>` entity can be used to distinguish stimulus files stored in the `stimuli/` directory.

This entity is only applicable to stimulus files.
type: string
format: label
annotation:
name: annot
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display_name: Annotation
description: |
The `annot-<label>` entity can be used to distinguish different annotations
of the stimulus data.

This entity is only applicable to stimulus files.
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A parallel to investigate here is _events.tsv files, i.e. those could also be created/annotated across various dimensions. ATM they would just "flatten" them into this single file with some column potentially disentangling those dimensions for different annotations (e.g. low level properties of visual stimuli vs higher level cognitive concepts vs responses). So it feels to me it might be applicable there too.

But with that it somewhat begs me to think about some possible alternative name/concept but I find none and there be none ;)

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Since we already ran into discussion either desc could be in effect used as desc (and we have example in bids of _desc-autoannot), it would be valuable to describe here the difference from desc, e.g. annot is more specialized in providing annotations to the stimuli/events whenever desc is more about processing of the data. So _annot-chatgpt would be preferable over _desc-chatgpt as would symbolize annotation over some other chatgpt driven processing (e.g. prompted chatgpt for some analysis of data/stimuli)

type: string
format: label
2 changes: 2 additions & 0 deletions src/schema/rules/entities.yaml
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Expand Up @@ -30,3 +30,5 @@
- density
- label
- description
- stimulus
- annotation