ga4gh / ga4gh/phenopacket-schema

How to model Disease Severity

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Dominant language
Java
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Description

We want to use phenopacket schema to study disease severity. For example severity of depression. However, its not obvious how to do this with the schema.
We considered the `disease_stage` on the `Disease` block, but that implies a progression, as it commonly happens in cancer. Diseases like Depression fluctuate in severity and do not strictly progress, hence the `disease_stage` does not seem ideal.

We think, this belongs to the `Disease` block and not `Interpretation > Diagnosis`, because interpretation represents the outcome of genomic analysis.

Could you add a severity field as it is in the `PhenotypicFeature`?

Contributor guide

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Research direction

Review how the phenopacket schema defines the Disease block, Interpretation > Diagnosis, and severity on PhenotypicFeature. Compare those existing modeling choices and their implications for fluctuating disease severity, then document a compatible schema design and its validation requirements.

Written by the indexing model from the issue text.

Assessment

Tech stack
java
Domain
backend-api-design
Issue type
Feature
Difficulty
5/5
Estimated time
Over a week
Activity status
Quiet
Clarity
Mostly clear
Newbie friendliness
45/100

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