ga4gh / ga4gh/phenopacket-schema
How to model Disease Severity
- Dominant language
- Java
- Stars
- 101
- Forks
- 34
- PR merge metrics
- No merged PRs in 30d
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
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