ga4gh / ga4gh/phenopacket-schema

VitalStatus.Status = Alive is ambiguous

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Java
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Description

If we read VitalStatus.Status = Alive then this could mean several things:

  1. The individual was alive when the phenopacket was created
  2. The individual was alive at the TimeAtLastEncounter
  3. The individual is alive at the very moment someone reads the Phenopacket
  4. The individual was alive when one of the ExternalReferences was written

I note the guidance (https://phenopacket-schema.readthedocs.io/en/latest/vital-status.html) says

This element can be used to report whether the individual is living or dead at the timepoint when the phenopacket was created

But for many uses of Phenopackets that won't be known, and it will just be known that someone was alive at a particular point of time in the past, or when they were 60 years old etc.

It seems to me that there should be an (optional) way to link a TimeElement to the VitalStatus.Status = Alive data

Contributor guide

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First steps

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  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start by reading the vital-status guidance and the definitions of VitalStatus.Status, TimeAtLastEncounter, ExternalReferences, and TimeElement in the Phenopacket schema. Determine how an optional time association for Alive should be represented and how its meaning is documented; done means the schema and guidance remove the ambiguity without changing the existing interpretation.

Written by the indexing model from the issue text.

Assessment

Domain
backend-api-design
Issue type
Feature
Difficulty
5/5
Estimated time
Over a week
Activity status
Active
Clarity
Mostly clear
Newbie friendliness
35/100

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