Standardized Organism Selection for Reliable Microbial Typing

[karlnyr]

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:

• 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.