RDBMSes aren't flat. The R part sees to that. What you need is:
Table Entity
------------
ID
Table EntityData
----------------
EntityID
MatrixRow (1, 2, 3...)
MatrixColumn (A, B, C, D...)
Value
Entity:EntityData
is a one-to-many relationship; each cell in the matrix has an EntityData row.
Now you have a schema that can be analyzed at the SQL level, instead of just being a data dump where you have to pull and extract everything at the application level in order to find out anything about it.
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