Diagnosis confidence level definitions and interpretation

Last updated: September, 2016

NPDN diagnosticians assign levels of confidence to each diagnosis that is uploaded to the National Data Repository (NDR). This document provides the definitions and guidelines on interpreting the confidence level information.

The NDR uses four terms to define confidence

Confirmed - The diagnosis was derived using molecular technologies, serological testing, morphological observations, and/or other techniques as listed in the NPDN Lab Method Dictionary which allowed for the confirmation of the organism to a taxonomic level including Order, Family, Genus, species and/or race or pathovar. The confidence term assigned applies to the chosen taxon level. The species term is not relevant to taxonomic confirmations at the level of Order or Family, so assignment of confirmation terms to sp. or spp. is unnecessary. 

Suspected - Symptoms of a specific plant problem were present but evidence of that causal agent could not be confirmed at this time. In pest and plant identification situations, this term is used when specific characteristics of a specimen are insufficient for confirmation. This term may also be used at the species level if confirmations cannot be made. This term is frequently used with abiotic entries when confirmatory evidence based on additional tests such as tissue/soil/water analyses, and/or information is not available.

Not Detected - The pathogen/pest was not detected on this sample at the time of testing using molecular technologies, serological testing, morphological observations, and/or other techniques as listed in the NPDN Lab Method Dictionary 

The sample may have been submitted as a suspect sample or as part of a survey project or the sample may have been checked for a specific pathogen/pest frequently associated with that host.

Undetermined - Although a suitable sample was received, a reliable result could not be achieved. Example cases where this term is appropriate:

• Inconclusive test results
  • Testing procedure (i.e., molecular technologies, serological testing, morphological observations, and/or other techniques as listed in the NPDN Lab Method Dictionary) may not have worked correctly and there was no sample material remaining to perform the test again.
  • The testing protocol was not available to run the test
• The pathogen or pest could not be identified to genus and/or species level, including in situations such as lack of key resources/expertise, difficulty identifying life stage or sex, or the known presence of cryptic species.
• The abiotic/biotic causal factor could not be determined and suspected is not an acceptable option

Interpreting Confidence levels when searching data in the NDR

Because the NDR accepts data for undetermined, suspected, and not detected diagnoses, NDR users must always be mindful of the confidence levels of the diagnosis they are searching. 

In most data queries, users must pay attention to the Overall Confidence Level (OCL) of the diagnosis. Most query tools in the NDR allow the user to filter data based on the OCL. Data requests will also provide this information.

For cases when diagnosis are not fully confirmed, the NDR may also contain identifications that have different confidence for the genus and species. In some cases described below, NDR users may chose to request or query genus and species confidence levels separately.

Browsing confirmed genus:

The goal of allowing the entry of different confidence levels for the genus and the species, is to allow diagnosticians to indicate if they are certain about a genus diagnosis, even if they are uncertain about the species diagnosis.

If an end user wants to find all cases of confirmed genus irrespective of species or species confidence, they must request records of all confirmation levels and inspect genus and species confidence levels separately.

Historical data:

Before 2022, any combination of two confidence levels were allowed in the NDR. As a result, over the years, diagnosticians accidentally entered some confusing and ambiguous confidence information. For instance, users may have diagnosed ‘Bipolaris cynodontis’ with genus confidence 'suspected', and species confidence 'confirmed'. The NDR labels this diagnosis with OCL = 'confirmed' even if this is not really clear from the reported genus confidence.

Most of these ambiguous combinations of confidence level are corrected when using the OCL. For example, if an entry has genus ‘Not Detected’ or ‘Undetermined’ the OCL ignores the species confidence and uses only the genus confidence. However, if a user wants to be thorough in interpreting historical data, they should query or request both genus and species confidence levels and screen for inconsistencies.

Other recommended reading to understand the NDR data:

• Introduction to the National Data Repository
• Understanding diagnostic data in the NDR
• Diagnostic method description as entered in the NDR

If you have questions or want to report a problem in this page please contact the NPDN National Data Committee at data@npdn.org.

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