Performing manual joins where one child has many parents and possibly on different childs


I would like to find the best efficient approach on performing manual
joins. A little background:

Our documents are updated quite frequently and they are rather large
(reason why we don't nest them). In addition, one document may be related
to two or more other documents (may be on different shards). We thought of
removing the current parent-child filters and perform the joins ourselves
to provide more flexibility.

Here is on scenario:

VariableQuery -> StudyQuery -> NetworkQuery

There are of course IDs that relate each document to the other.

NetworkQuery's IDs are used to refine the StudyQueries which in turns its
IDs are used to refine the main (root) VariableQuery.

An expert guideline/suggestion/solution will be greatly appreciated,

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