A method for processing and organizing pharmaceutical data from a plurality of sources. Batch files are submitted to a data processor electronically, such as via an electronic communications network. The batch files are checked for validity, then stored in a holding database. Records are read from the batch file and checked for errors such as relational integrity. Records having errors are noted in an exception file and held for correction, while records having no defects are placed into a common format and loaded into a data warehouse. Records having minor defects may also be loaded into the data warehouse pending correction of the defects.