Abstract: The present invention provides an integrated data system for processing deposition and annotation of data such as three dimensional macromolecular structure data. The system is based on a new community data standard referred to as meta data. The meta data structure provides data or information about other data. Unlike the previous PDB data format, in the present invention PDB both the syntax and semantics of the PDB data standard are rigorously defined and encoded in meta data dictionaries which are fully software accessible. The data processing system of the present invention uses meta data at every functional step beginning with data collection.