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cidgoh / DataHarmonizer

A standardized browser-based spreadsheet editor and validator that can be run offline and locally, and which includes templates for SARS-CoV-2 and Monkeypox sampling data. This project, created by the Centre for Infectious Disease Genomics and One Health (CIDGOH), at Simon Fraser University, is now an open-source collaboration with contributions from the National Microbiome Data Collaborative (NMDC), the LinkML development team, and others.
MIT License
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CanCOGeN template: adding a new null value to the Diagnostic PCR Ct Value fields #206

Closed griffie closed 3 years ago

griffie commented 3 years ago

Right now the Diagnostic PCR Ct Value fields allow for numerical values and the standard set of null values to be entered. However, sometimes labs will carry out an RT-qPCR test and get an indeterminate result. Indeterminate results don't really have an equivalent in the current set of null values (Missing, Not Applicable, Not Provided, Not Collected, Restricted Access) as the info is applicable, was collected and provided, but the result is unclear.

We would like to add a new null value for the PCR fields only (but there are 3 i.e. Diagnostic PCR Ct Value 1, Diagnostic PCR Ct Value 2, Diagnostic PCR Ct Value 3). That value is called "Indeterminate".

This value should export to the LIMS export format directly as it is in the DH (i.e. Indeterminate).

Thanks!

ddooley commented 3 years ago

Ok, I think this only needs a vocabulary update - to add this value to the null value list for those fields. Has it been added there?

griffie commented 3 years ago

Yessir, indeed it has.

ddooley commented 3 years ago

Ok its updated and will be included in next release

ddooley commented 3 years ago

Hmm, I'm seeing no null value lists for Diagnostic PCR Ct Value 1 etc. I would add them, and add "Indeterminate" to their lists. This provides a pulldown menu for these fields.

ddooley commented 3 years ago

Done