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Reprocess PD datasets with the new assessment tool library #220

Open
8 of 11 tasks
Tracked by #232
surchs opened this issue Jan 10, 2025 · 2 comments
Open
8 of 11 tasks
Tracked by #232

Reprocess PD datasets with the new assessment tool library #220

surchs opened this issue Jan 10, 2025 · 2 comments

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@surchs
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surchs commented Jan 10, 2025 •
edited by alyssadai
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  1. using the current annotation tool, re-annotate the following datasets using the SNOMED vocabulary for assessments

    • PPMI dataset
    • QPN dataset
      • obtain latest wide-format phenotypic tabular file
    • Calgary dataset
      • note: phenotypic & BIDS data are only on Compute Canada for now, and no Nipoppy processing info is available yet
      • BIDS conversion still in process

  2. using the Neurobagel CLI v0.4.0 (latest), regenerate JSONLD files (running the pheno, bids, and derivatives commands) for:

  • Create cronjob to auto-sync PD files from BIC to fairmount server, and verify data paths
    • daily cronjob installed on BIC under Alyssa's account
@surchs surchs added the flag:schedule Flag issue that should go on the roadmap or backlog. label Jan 10, 2025
@alyssadai alyssadai moved this to Backlog in Neurobagel Jan 14, 2025
@alyssadai alyssadai removed the flag:schedule Flag issue that should go on the roadmap or backlog. label Jan 15, 2025
@surchs
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surchs commented Jan 16, 2025

@michellewang is working on PPMI and also adds new pipelines for the derivatives

@alyssadai
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@michellewang has also kindly agreed to re-annotate the Calgary dataset 🙏🎉

@surchs surchs mentioned this issue Jan 21, 2025
Open
11 tasks
@alyssadai alyssadai moved this from Backlog to Implement - Active in Neurobagel Jan 21, 2025
@alyssadai alyssadai moved this from Implement - Active to Implement - Track in Neurobagel Jan 21, 2025
@alyssadai alyssadai mentioned this issue Jan 21, 2025
Open
7 tasks
@rmanaem rmanaem moved this from Implement - Track to Specify - Done in Neurobagel Jan 24, 2025
@alyssadai alyssadai changed the title re-annotate the datasets with the new assessment tool libraries Reprocess PD datasets with the new assessment tool libraries Jan 25, 2025
@alyssadai alyssadai changed the title Reprocess PD datasets with the new assessment tool libraries Reprocess PD datasets with the new assessment tool library Jan 25, 2025
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