Dates and Durations

There are a variety of ways in which we wish to record temporal information in a phenopacket

• Recording the time of an event such as the day of birth
• Recording the timing of condition, such as the onset of a disease or phenotype

These may be recorded in a qualitative or quantitative fashion. For qualitative information, we make use of ontologies such as the HPO or HsapDv, which provide ready-made bins according to stages of a life cycle.

For quantitative information, we allow differing levels of precision, such as the date or the date and time. We always use ISO-8601 for recording these. In some contexts we also allow relative quantitative information, such as an age. Because we do not always know the precise dates, we also allow the specification of onsets and offsets using temporal regions.

We usually allow partial information. For example, we may have information on the onset of a disease, but not when it ceased. We also allow the combination of information, for example recording onset both as a phenotype term, and as a date.

Model

See the reference implementation for more details.

Disease and Phenotype are both subtypes of Condition

A Condition can have both an onset and an offset, both of which are instances of a TemporalRegion

A TR can be specified using a combination of

• ontology classes
• a start_time and an end_time

Examples

See age of onset examples