1. A computerized system for manipulating data sets, comprising: a hardware-based processor; and a data repository that contains the data sets and one or more layers of metadata of the data in the data sets, comprising: a class module configured to define at least one class of elements and store the class; an attribute module configured to define one or more attributes and store the attributes; a class attribute module configured to define and store one or more class-attribute associations between at least one of the attributes and the class; an element attribute module for the at least one class configured to: define and store the attributes of the elements in the class; and transmit the attributes and the elements; an element module configured to receive the transmitted attributes and elements from the element attribute module, store the attributes and elements, and uniquely identify the elements, wherein the elements are identified by unique element identifications; an element relation module configured to store one or more relationships between the elements in the element module; an element history module configured to store one or more indicators of a modification to the elements; and an element document module configured to store formatting data for grouping a subset of the elements.