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Standardized Organism Selection for Reliable Microbial Typing #4217

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karlnyr opened this issue Feb 18, 2025 · 0 comments
Open
7 tasks

Standardized Organism Selection for Reliable Microbial Typing #4217

karlnyr opened this issue Feb 18, 2025 · 0 comments

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@karlnyr
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karlnyr commented Feb 18, 2025

As a production member,
I want to restrict the species selection to validated organisms and require a reference for non-validated organisms,
So that we ensure data consistency, reduce errors, and streamline the typing workflow.

Work Impact

  • Is there currently a workaround for this issue? If so, what is it?
    • Customers manually enter species names in the “Other species” column, which can lead to misspellings and inconsistencies.
    • We rely on customers to provide references for new species, but there is no validation process.
  • How much time would be saved by implementing this feature on a weekly basis?
    • For MWR, we in production are required to produce a passing QC result in the microsite QC report. This requires us to manually check the suggested species of a sample using Kraken, which takes perhaps 10 minutes per sample. However, after that, we also have to rerun the whole analysis for the sample, which takes hours.
  • How many users are affected by this issue?
    • The bioinformatics production team and all users handling microbial typing requests.
  • Are customers affected by this issue?
    • Yes, customers experience inconsistent handling of non-validated organisms, which can lead to uncertainty in typing results.

Acceptance Criteria

  • The “Species” column allows only a predefined list of validated organisms or Other. The validated set of organisms, and their reference genomes are list here:
Image
  • Rename the validated organism so that:
    • The internal ID is the short name
    • The Name is the full-length name
    • Remove the duplicated K. pneumoniae entry, keep the one with NC_016845.1 as the reference genome.
  • If a validated organism is chosen, we use the value of the reference for the organism in StausDB
  • If “Other” is selected in the order form or the order portal, a reference must be provided.
  • The “Other species” column is removed from the order form.
  • StatusDB only stores validated organisms and references for better data management.
  • Orders do not create new entries in the "Organism" table

Notes

  • Additional information.
  • Dependencies.
  • Related user stories.
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