1. A computerized system for manipulating data sets, comprising: a processor; and a data repository, the data repository being adapted to process, retrieve, and store data contained in the data sets and one or more layers of metadata of the data in the data sets, comprising: an element module configured to store and uniquely identify a plurality of elements, wherein each of the elements is identified by a unique element identification; an element relation module configured to store one or more relationships between the elements in the element module; a class module configured to define at least one class of the 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; and a type definition module configured to define and store one or more types of the class, the attributes related to the class, and the relationships between the elements.