Table 2.

The HPO records the frequencies of phenotypic features in three different ways

Frequency categories
Term	ID	Definition
Obligate	HP:0040280	Always present, i.e. in 100% of the cases.
Very frequent	HP:0040281	Present in 80–99% of the cases.
Frequent	HP:0040282	Present in 30–79% of the cases.
Occasional	HP:0040283	Present in 5–29% of the cases.
Very rare	HP:0040284	Present in 1–4% of the cases.
Excluded	HP:0040285	Present in 0% of the cases.
Percentage of persons in which a phenotypic feature is observed
Percentage	x%	This is used to record frequency of a feature in a disease if the number of probands is not available, e.g. 42%.
Number of persons in a cohort in whom a phenotypic feature was observed
N of M notation	n/m	This is used to record how many persons with a certain disease were observed to have a given phenotypic feature represented by an HPO term, e.g. 5/13. This should be used only if the feature was ruled out in the remaining m-n individuals.

Frequency information can be used by differential diagnostic algorithms such as BOQA (62). If possible, HPO annotations are made with the precise counts, but percentages or overall frequency categories are used if that is all that is available. The frequency categories are aligned with those of Orphanet.