What makes up a good HPO term?

Deep phenotyping

The HPO is intended to support computational deep phenotyping, which can be defined as the annotation and analysis of the individual features of disease (Human Mutation 2012 PMID:22504886). HPO terms therefore do not describe disease entities, but rather the individual manifestations of the diseases.

What is the distinction between a disease and a phenotypic feature?

THe HPO considers a disease to be an entity that has a known or unknown cause, is characterized by one or more phenotypic features which can affect all or only a subset of individuals with the disease, a time course over which the phenotypic features may have onset and evolve, and in some cases one or more indicated treatments and a response to treatment. For instance, if the disease entity is the common cold, then the cause is a virus, the phenotypic features include fever, cough, runny nose, and fatigue, the time course usually is a relatively acute onset with manifestations dragging on for days to about a week, and the treatment may include bed rest, aspirin, or nasal sprays. In contrast, a phenotypic feature such as fever is a manifestation of many diseases. There is a grey zone between diseases and phenotypic features. For instance, diabetes mellitus can be conceptualized as a disease, but it is also a feature of other diseases such as Bardet Biedl syndrome. The HPO takes a practical stance and provides terms for such entities.

What is the desired level of granularity of an HPO term?

In general, each HPO term refers to a recognizable entity that occurs in multiple patients and often in multiple diseases. We do not try to create an HPO term for very specific manifestations in individual patients. For instance, the following description would be too detailed to be a good HPO term.

hamartomatous proliferation containing malformed hair follicles in various stages of development

Bundled terms

Each HPO term should describe a single abnormality. The following description is actually referring to at least three different manifestations.

irregularities in the number of spikes in the spike-wave complex , spike amplitude and in occurrence of fragmentation