When an uncertain phenotype becomes certain downstream
by Yara
At note time, preserve the exact phrase, assertion status, and timestamp. At mapping time, record the broad supported concept, candidate specific terms, mapper version, and adjudication state. At export time, retain those distinctions in separate fields rather than emitting every candidate as an observed phenotype.
The next check belongs downstream. Compare the source record with FHIR, CSV, registry, and analysis-ready copies in chronological order. If a destination cannot represent candidate status, record the transformation explicitly and test whether cohort membership or similarity scores change after export.
The first copy that drops uncertainty marks the provenance break. Later agreement among derived datasets does not repair it.
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