The National Data Repository (NDR) requires users to enter a confidence level for each diagnosis they submit. All users are probably quite familiar with the available values for confidence levels: Confirmed, Suspected, Not Detected, and Undetermined (Read the definitions here). However, for historical reasons, the NDR also allows the entry of identifications that contain different confidence for the genus and species levels (and in some cases, also the subspecies).
Unfortunately, before 2022, any combination of genus-species confidence levels could be uploaded to the NDR. There were no restrictions or standardization in the NDR or the LIMS as to what combinations of confidence levels made sense from a taxonomic or diagnostic point of view. As a result, over the years, the NDR accumulated some confusing and ambiguous confidence information. For instance, users may have diagnosed ‘Botrytis cinerea’ with genus confidence suspected, and species confidence confirmed. In cases like this, it’s unclear what the user intended to report.
Read the Guidelines on How to Assign Confidence Levels to the Diagnosis.
The problem of ambiguous data was identified some time ago, and a few steps had been taken to address it. However, it was not until 2021 that a working group took on the significant task of solving the problem of confidence combinations once and for all. During the 2021 IT/diagnostician meeting, the Confidence Level Working Group was established. The members were Clarissa Balbalian, John Bonkowski, Tania Brenes-Arguedas, Tom Creswell, Chandler Day, Mike Hill, Jen Olson, and Karen Rane. For months, they met to dissect the problem and brainstorm appropriate solutions. Then, they worked with CERIS and the LIMS committee to implement these solutions. The result is that the LIMS now restrict the combinations of confidence levels allowed to those that make diagnostic and taxonomic sense. Users for PDIS and PClinc may have observed the changes that have been implemented in their LIMS. The same restrictions will be implemented in the NDR at a later date.
To culminate their work and complement the technological solutions, the working group developed a document with comprehensive guidelines on how and when to use combinations of confidence levels when submitting data to the NDR. These guidelines have been published, and all diagnosticians are encouraged to review them here:
Read the Guidelines on How to Assign Confidence Levels to the Diagnosis.
