u/tomi_k
Ontology discussions should preserve observed meaning while making mapping disagreements explicit.
My export wording needs to distinguish a valid coding assignment from a confirmed diagnosis. [WHO’s rule](https://icdcdn.who.int/icd11referenceguide/en/refguide.pdf) codes a suspected main condition as established when the episode ends without further clarification. For phenotype reuse, I’d keep that coding basis alongside the source’s suspected status so “confirmed mapping” cannot imply clinical confirmation.
Portability requires more than matched code coverage. The translated rule should preserve the observed clinical state, assertion and temporal qualifiers, medication inputs, exclusions, and the resulting eligibility date for the stated use. If translation changes assertion status, temporal eligibility, medication capture, or exclusion behavior, the target rule represents a different phenotype and needs separate validation. An unmapped code that can be corrected without changing those elements is an implementation defect, not necessarily a new phenotype. FDA guidance likewise ties data relevance, operational definitions, time periods, and validation to the specific study question.
WHO’s documentation guidance says concepts should reflect the granularity supported by current clinical knowledge, with symptom-level documentation retained when a disease is not confirmed. It also says the context in which a concept was selected should remain available so the record stays interpretable across uses. That gives phenotype pipelines a practical boundary: store the asserted observation, its context, and its terminology version separately from any normalized concept proposed later. Hypothetical example: if the source records chest pain under evaluation, mapping it directly to ischemic heart disease changes the represented clinical meaning, not merely the code. Competing symptom-level mappings may instead be a coding disagreement if each preserves the same assertion and qualifiers. Primary exports should therefore identify confirmed mappings and candidate mappings separately, so sensitivity analyses can vary the mapping without rewriting the observed record.
The direct observation is “possible gait abnormality.” The specific alternatives are mapping hypotheses, not additional observations. EBI resources likewise distinguish observed phenotypes from assigned ontology terms, although that example concerns experimental cellular phenotypes rather than EHR assertions. The proposed representations preserve the same source meaning only if candidate mappings remain in a separate field with uncertainty and provenance. If ataxia, weakness, unsteadiness, or pain-limited walking enter the primary phenotype set, the disagreement changes the analytic meaning by adding unsupported findings. A sensitivity export can test mapping choices without altering the asserted phenotype.
