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Support multiple participant ID columns in tabular data #286

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alyssadai opened this issue Mar 26, 2024 · 2 comments
Open

Support multiple participant ID columns in tabular data #286

alyssadai opened this issue Mar 26, 2024 · 2 comments
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flag:discuss Flag issue that needs to be discussed before it can be implemented. someday Not a priority right now, but we want to keep this around to think or discuss more.

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@alyssadai
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We keep encountering TSVs that have a participant ID column without the sub- prefix required for BIDS subdirectories.
This makes sense, as most likely the phenotypic/tabular data will have preceded the BIDS conversion step for most datasets.

Right now, the only option for these kinds of tabular data to work with the Neurobagel CLI is if the data owner adds another column for the BIDS participant IDs, or modifies their existing participant ID column. This is probably not ideal, and also means that we are sometimes creating extra work for data owners only if they have imaging data in addition to phenotypic data.

We should consider having the CLI handle this work by automatically prepending sub- onto a given participant ID column if the prefixes don't already exist, before doing the imaging-tabular subject matching check.

@alyssadai alyssadai added flag:discuss Flag issue that needs to be discussed before it can be implemented. flag:schedule Flag issue that should go on the roadmap or backlog. labels Mar 26, 2024
@alyssadai
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We need to think about the scenario where some subjects in the tabular file have BIDS data, but not all.

@alyssadai alyssadai changed the title Support non-BIDS participant IDs in tabular data? Support multiple participant ID columns in tabular data Mar 27, 2024
@alyssadai alyssadai removed the flag:schedule Flag issue that should go on the roadmap or backlog. label Mar 27, 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.
When you review, please reread the spec and then apply one of these three options:

  • prioritize: apply the flag:schedule label to suggest moving this issue into the backlog now
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  • archive: sometimes an issue has important information or ideas but we won't work on it soon. In this case
    apply the someday label to show that this won't be prioritized. The stalebot will ignore issues with this
    label in the future. Use sparingly!

@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 Jun 11, 2024
@alyssadai alyssadai added someday Not a priority right now, but we want to keep this around to think or discuss more. and removed _flag:stale [BOT ONLY] Flag issue that hasn't been updated in a while and needs to be triaged again labels Sep 28, 2024
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Labels
flag:discuss Flag issue that needs to be discussed before it can be implemented. someday Not a priority right now, but we want to keep this around to think or discuss more.
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