Normal Findings

The HPO contains terms that denote abnormal phenotypic features. There are no terms such as Normal renal echogenicity.

How can HPO be used to state that a clinical finding was normal?

To state for instance, we state that the abnormal term was excluded. For instance, to state that renal echogenicity was normal, we would state

Abnormal renal echogenicity (HP:0033130): Excluded.

There are many ways that HPO-based databases can represent this information.

Tabular

For instance, the following table shows three HPO terms and eight patients in whom an HPO term was observed, excluded, or for which no information was available ("na")

HPO Term	P1	P2	P3	P4	P5	P6	P7	P8
Primum atrial septal defect (HP:0010445	excluded	na	observed	observed	na	observed	observed	na
Hypernatremia (HP:0003228)	observed	observed	na	excluded	na	observed	na	excluded
Splenomegaly (HP:0001744)	na	excluded	excluded	eobserved	observed	na	observed	na

GA4GH Phenopackets

The Phenopacket Schema was designed to represent clinical information using HPO terms. The Phenopacket Schema contains an element called PhenotypicFeature that contains a field to indicate whether a feature was excluded or not. This is the recommended way to represent HPO-based clinical data.

What to exclude

It is good to annotate observed findings as specifically as possible (e.g., Renal cortical hypoechogeneity HP:0033133 rather than Abnormal renal echogenicity HP:0033130). However, if say sonography was used to investigate the kidney, then one provides more information by indicating that Abnormal renal echogenicity HP:0033130 was excluded because there are several different types of abnormal renal echogenicity (child terms) that are also excluded.