Condition

[ShahimEssaid]

Discussion thread for page: https://phenopackets-analysis.readthedocs.io/en/latest/domain-entities/condition.html

[pnrobinson]

It seems Disease can easily be modeled as a FHIR Condition

Disease.term = Condition.code
Disease.onset = Condition.onset
Disease.disease_stage = Condition.stage

The v1 phenopacket has a fourth element, tnm_finding. However, it seems that this could be subsumed under disease_stage and it was perhaps a mistake to include this element. Therefore, I would suggest for our IG that we model just the first three elements of Disease as a Condition. @ShahimEssaid

[pnrobinson]

@ShahimEssaid it seems that we only need to require that the Condition use an ontology term to describe the disease. The default is a 0..1 cardinality. So I think that all we need to do is to stipulate that the cardinality is 1..1.
The Phenopacket fields for disease onset and stage are optional, and so for the IG, I do not think that we need to make them required.
There is another question of how to translate disease codes into codes that can be used for rare disease genomics, and so if we wanted to, we could stipulate a code set using MONDO. But knowing the disease is not required for exome diagnostics if we have phenotypes, and if we knew the exact disease, we would not be doing diagnostics. I will make a PR for the SturcutreDefinition of disease -- I think we can keep it simple.