Matthew Brush

SO has a sequence attribute hierarchy describing variant origin. SO_0001762 (variant origin) ---SO_0001781 (de novo variant) ---SO_0001778 (germline variant) ---SO_0001775 (maternal variant) ---SO_0001776 (paternal variant) ---SO_0001779 (pedigree-specific variant) ---SO_0001780 (population-specific...

2018-02-07 update: No modeling implemented for these areas yet in GENO, as we have not ingested sources with these data types which would provide impetus and requirements for doing so.

Thanks for the feedback @pfabry. I agree with your proposal but would change the axiom on this class to real 'is about some information content entity', and adjust your proposed...

A major value of this type system will be to enable interoperability with other, less granular datasets that rely on evidence codes as a primary means of describing assertion evidence...

These questions touch directly or indirectly on **four aspects** of CriterionAssessments (CAs) and the evidence they provide for target VariantInterpretations (VIs), which we have identified as important in our previous...

@bpow re: the idea of capturing evidence direction using three properties (has_supporting_evidence, has_refuting_evidence, has_inconclusive_evidence) > On the other hand, those of us in the relational database-ish world balk a bit...

@bpow regarding: >We would also have to be careful about how we specify how those terms relate between evidence and information... For assertion A, evidence line B, information C. I...

I think I agree with Chris' point that from the ClinGen/ACMG perspective, it is not critical to assign strength in these cases. The ACMG guidelines capture strength of evidence only...

Just posing a devil's advocate perspective for posterity here, w.r.t. the suggestion that: > Would you consider (as long as you are changing "data" to "information") renaming this to has_information...

Hi. Sorry took so long to reply here. We do indeed, and and will explore alignment with or re-use of CIO.