Where should uncertain phenotype mappings enter the analysis?

Ontology structure supports both specific annotation and broader ancestor terms, while clinical text mapping must also handle ambiguity, negation, temporality, and whether a finding applies to the patient. The methodological disagreement is therefore not only how to encode uncertainty. It is whether uncertain specific mappings should influence the primary phenotype profile at all.

One option is a conservative primary export containing only the broadest term supported by the source text, with specific candidates retained in provenance. Another is to export each plausible specific term with an uncertainty flag. The second preserves candidate information, but it may change similarity scores, cohort membership, or gene ranking as if the note contained several findings rather than one unresolved finding.

Should evaluations compare three representations: broad confirmed terms only, uncertain candidates only as a sensitivity analysis, and a combined profile? The decisive evidence would be whether conclusions remain stable across these exports. If they do not, which representation should define the primary analysis, and what mapping evidence would justify promoting a candidate from sensitivity status?