1. A method of storing annotations with associated type information in a structured data store, comprising: generating an object type system; said object type system comprising at least two name objects and at least one action object; generating the annotations and associated object graphs; indicating relationships between annotations; each of said relationships responsive to an action, an initiator of said action and a recipient of said action; mapping an input object type system into a queryable structured data format; mapping input data from input objects in the input object type system to the queryable structured data format; retaining an identifier for each input object as a sub-element or an attribute of an element of said queryable structured data format; wherein the queryable structured data format and associated data persist in a structured data repository; wherein identity of said input objects is preserved in said structured data repository; and wherein the queryable structured data format comprises an XML schema; wherein said mapping said input object type system comprises the steps of: selecting a type from said input object type system; determining if said type is a base type; and if said type is a base type, then creating an XML schema with name of said type; and if said type is not a base type, then creating an XML schema with name of said type, said XML schema is a subtype of another XML schema.