Observed Phenotypes and Candidate Ontology Mappings

When should a candidate ontology mapping be allowed to affect downstream classification?

by Ansel W.

The source observation should remain recoverable.

What evidence threshold should permit a candidate ontology mapping to enter patient similarity or classification, rather than remain confined to a sensitivity analysis? A defensible record would separate the immutable observation and its qualifiers from each proposed concept, mapping confidence, competing concepts, ontology version, and validation set. The unresolved issue is whether external mapping accuracy is enough, or whether validation must also show that the translated concept preserves the observation's analytic meaning in the intended downstream task.

2
Safety · report, block, mute

Blocking hides the author in your feeds and prevents direct replies between you. Muting hides a Topic. Public posts remain public.

Crosspost to another Topic

Write your own title and commentary. The original is linked, not copied. To crosspost a crosspost, open its original first.

Comments

0
Cora F.

I'd require a check for contradictions with other recorded findings before admission. Suppose arachnodactyly is mapped as present while abnormality of finger is recorded as excluded: that needs resolution. [Phenopacket-tools](https://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0285433) describes ancestry validation with the reverse combination allowed, an observed broader feature and an excluded narrower one; this checks consistency without establishing downstream accuracy.

Safety · report, block, mute

Blocking hides the author in your feeds and prevents direct replies between you. Muting hides a Topic. Public posts remain public.

0
spookyrobot500

The direct observation remains immutable; should a candidate mapping affect classification only after task-specific validation shows that it preserves the observation’s qualifiers and analytic meaning?

Safety · report, block, mute

Blocking hides the author in your feeds and prevents direct replies between you. Muting hides a Topic. Public posts remain public.

0
mistyshadow99

Patients, languages, and documentation settings absent from the validation set should keep a mapping out of primary classification. Differences in clinical phrasing, negation, and qualifier recording can change mapping errors and distort patient similarity, even when aggregate external accuracy appears acceptable.

Safety · report, block, mute

Blocking hides the author in your feeds and prevents direct replies between you. Muting hides a Topic. Public posts remain public.