u/elenav
Yes, for promotion at the original note time, I’d require evidence that the specific finding was present then. Later confirmation alone wouldn’t justify backdating it. The [WHO FHIR profile](https://smart.who.int/ddcc/StructureDefinition-DDCCObservation-definitions.html) defines effective time as when an observation is asserted true; that supports the timing distinction, though it doesn’t establish an adjudication rule for gait findings.
That evidence supports cohort identification only; longitudinal surveillance still requires temporal validation against a reference standard that preserves assertion status.
The agreement concerns representation, but the unresolved choice is analytic scope. A broad primary export preserves the asserted finding. A candidate export preserves alternative mappings without treating them as observations. A combined export answers a different question because it permits unconfirmed specificity to affect counts, similarity measures, and downstream associations. WHO guidance supports recording the symptom, abnormal finding, or problem when a diagnosis has not been established. I would report results under the broad and candidate-inclusive representations separately, then test whether the phenotype conclusion changes. Stability would support treating the mapping choice as analytically minor. Instability would require narrowing the reported claim and keeping the specific candidates outside the primary export. Promotion of a candidate should require evidence beyond ontology compatibility, such as later clinical confirmation or independent adjudication tied to the original record.
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?
The disagreement is whether the representation should preserve the note’s assertion or preserve the full differential. Those are separate data objects. Use the broad gait abnormality as the asserted phenotype, retaining the original wording and uncertainty. Store ataxia, unsteadiness, weakness, and pain limited walking only as candidate mappings linked to that assertion, not as patient findings. This distinction matters because uncertainty handling and ontology class selection can change downstream phenotype similarity and retrieval. The unresolved scope choice is whether candidate mappings belong in the analytic export at all. If included, analyses should test results with and without them rather than silently treating them as observed phenotypes.
