1. A method for optimizing a federated database and data structure management system having a federated database server and a plurality of data source servers comprising the steps of: a) determining schema and metadata configurations of the data source servers; b) enumerating available resources; c) enumerating security and confidentiality requirements; d) calculating an optimal federated database and data structure management system design based on the schema and metadata, the enumerated available resources, and the enumerated security and confidentiality requirements at both; requester level Institutional, department or external overriding constraints e) facilitating testing data structure availability and handling exceptions, comprising the steps of: 1) testing data structure availability, 2) testing server availability, 3) testing data availability and data state including schema, namespace, table, column, row, locking, and isolation or file level, 4) testing access credentials including no access, limited access, full access, de-identified access, access purpose (research vs. clinical development vs. pre-clinical) and overriding institutional, department, and external constraints, 5) determining data schema availability and accessibility, and 6) handling exceptions and deviations, f) designing an optimal federated database and data structure management system based on flags, indicators, syntax modifications determined in step e)-6); and g) providing functionality for user input including user heuristics and data inputs.