More complex ways of composing study groups

[mbrush]

Originally posted by @jsstevenson in #234 (comment):

I can't claim credit for this notion, but I've been asked to relay it. The defining characteristics of a StudyGroup are provided as an array in the characteristics property, and are "shared by all members of the StudyGroup, representing a criterion for membership in the group" (source). What if I want to express allele frequency for a cohort where members have either characteristic A or characteristic B? What if I want to say that the members have characteristic A but not characteristic B? And, maniacally, what if I have a cohort consisting of (A and not B) or (C and D)? Are these reasonable concepts to want to represent? And if so, how can StudyGroups be defined now in a way that minimizes API breakage if support for this is introduced in the future?

[mbrush]

Responses from original post:

From mbrush

Thanks for the comment James. These use cases were indeed considered, and a prior version of the StudyGroup class took a Characteristic object as its value, which included attributes that let us do some the things you describe. (You can get a sense for what this class looked like from the SEPIO model here, on which the core VA model is based). However, because the Characteristic class was not required for initial implementations, the simpler MappableConcept was used in its place. If this is a real need for your (or any) application, let us know and we can propose a more expressive modeling pattern (like SEPIO Characteristic) for review.

_From jsstevenson

Thanks @mbrush. I'm spending part of this week reviewing some of the scientific outputs associated with our project to see if there's a conceivable need at this juncture, but I haven't found anything yet that goes beyond an enumeration of multiple shared traits, which is compatible with the class in its current form.

[mbrush]

Related comment from @rhdolin in the ballot release discussion:

Would be useful to further standardize StudyGroup.characteristics. As a future endeavor, it would be very helpful to flesh out / standardize certain group characteristics, particularly those related to ancestry/race/ethnicity so that we can better compare, for instance, population allele frequencies or polygenic score.

Agreed, and this will come in time as we address issues around specifying terminology standards and constraints for values in Mappable Concepts and Coding objects, per issue #248.

[mbrush]

Keeping this open as we will have to update the initially proposed Characteristic model to accommodate new use cases coming from the GREGOR consortium project, that require more precise and expressive ways to represent the boolean logic for describing cohorts/study groups.