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Warn about BIDS ID matching if dataset has imaging data #34

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alyssadai opened this issue Sep 26, 2024 · 3 comments
Open

Warn about BIDS ID matching if dataset has imaging data #34

alyssadai opened this issue Sep 26, 2024 · 3 comments
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documentation Changes only affect the documentation usability Issue affecting user or developer experience.

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@alyssadai
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At the moment, if a user annotates a non-BIDS ID column in their phenotypic TSV as the participant ID, but then wants to include BIDS data in their JSONLD at the CLI step, they will need to go back and 1) add a new column with BIDS IDs to their TSVs and 2) re-annotate the TSV. This is pretty annoying, so we should instead have a clear warning during annotation that if a dataset has BIDS data that needs to be harmonized (or maybe if the user knows they intend to BIDSify data?), they should first generate and add BIDS IDs to the TSV before proceeding w/ the annotation.

@alyssadai alyssadai added the documentation Changes only affect the documentation label Sep 26, 2024
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We want to keep our issues up to date and active. This issue hasn't seen any activity in the last 75 days.
We have applied the _flag:stale label to indicate that this issue should be reviewed again.
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@github-actions github-actions bot added the _flag:stale [BOT ONLY] Flag issue that hasn't been updated in a while and needs to be triaged again label Dec 11, 2024
@alyssadai alyssadai added the usability Issue affecting user or developer experience. label Feb 11, 2025
@rmanaem rmanaem transferred this issue from neurobagel/legacy_annotation_tool Feb 11, 2025
@rmanaem
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rmanaem commented Feb 11, 2025

This is good to discuss further and implement as part of the validation.

@alyssadai
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Sounds good @rmanaem. To clarify, I think a simpler implementation that doesn't require input validation would be to always display a warning message (somewhere on the initial column annotation page?) that if the dataset also has BIDS imaging data that the user intends to harmonize with Neurobagel, the user should ensure that their uploaded tabular file contains matching subject IDs.

@github-actions github-actions bot removed the _flag:stale [BOT ONLY] Flag issue that hasn't been updated in a while and needs to be triaged again label Feb 12, 2025
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Labels
documentation Changes only affect the documentation usability Issue affecting user or developer experience.
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