BII-Data-Manager is a standalone java application, that validates ISA-Tab formatted reports and persist encoded information to database backend. It relies on Hibernate Object persistence broker framework to convert objects into HQL statement for persistence. It is therefore encesassary to provide BII-Manager with database connection information as well as information to write the database index and move the data files associated with ISA-Tab formatted metadata.

BII-Data-Manager also performs security and access rights managements. BII-Data-Manager also enables database reindexing as well as dataset tagging to highlight those compliant with MIBBI checklists.