Closed julesjacobsen closed 3 years ago
This was discussed during the last pedigree call and we agreed that affected
should be optional
rather than not recommended
, which was a relic from the version in which there was an additional (preferred) method for annotating affected status.
In the 2021-01/model.md the
affected
field on an individual is marked as "not recommended", but nonetheless included for backwards compatibility.How are users supposed to indicate which individuals are
affected
with the Pedigreereason
in the case of something like a rare-disease diganosis? It these cases you don't know the condition, but a specialist has determined that individuals A and B are both affected with a common condition. You can't reliably use a collection of phenotype terms either as these may be different making downstream software's job really hard to ascertain which individuals in the pedigree are affected. Hence the use of a boolean flag or status codes.I agree that this is annoying in that it means that the pedigree is, like with the
proband
andconsultand
, a relative thing which limits reuse.To remedy my first point, it might be simplest to make the field "optional". The Pedigree
reason
field is marked optional for this reason so it seems odd to not recommend it in the Individual.To address the point of relative use of a pedigree, adding another data structure to hold the 'unbiased' pedigree along with identifiers indicating the
proband
,consultand
,reason
andaffected
. This would make thePedigree
a simple statement of relationships and the other thing would encode the data necessary for a particular use/analysis of thePedigree
e.g.
PedigreeContext
Pedigree