ga4gh / ga4gh/phenopacket-schema
VitalStatus.Status = Alive is ambiguous
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- Dominant language
- Java
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- 101
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Description
If we read VitalStatus.Status = Alive then this could mean several things:
- The individual was alive when the phenopacket was created
- The individual was alive at the
TimeAtLastEncounter - The individual is alive at the very moment someone reads the Phenopacket
- The individual was alive when one of the
ExternalReferenceswas 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
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- 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