Information and Computing Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
The Object-Protocol Model (OPM) data management toolkit (see http://gizmo.lbl.gov/opm.html) provides facilities for rapid development, comprehensive documentation, and flexible exploration of molecular biology databases (MBDs). OPM schemas can be translated into relation database definitions for a variety of commercial relational DBMSs, or can be retrofitted to existing relational or ASN.1 MBDs, thus providing semantically enhanced views of the underlying MBDs. In addition to OPM schema compilers and retrofitting tools, the OPM toolkit includes query interpreters for an OPM-based subset of the ODMG standard for object-oriented query languages, and a Web/Java interface for browsing, querying, and updating MBDs.
MBDs that have been developed or retrofitted with OPM can be assembled in a federation. An OPM multidatabase query system (OPM*QS) provides facilities for constructing and querying such federations. OPM*QS allows browsing the structure, connections, and documentation of MBDs in a federation, thus aiding in the construction of complex multi-database queries. In addition, OPM*QS incorporates a powerful query engine, capable of performing complex data manipulations that are not supported by the underlying DBMSs.
The OPM toolkit has been applied for developing several MBDs, notably GDB 6 and the new version of PDB, 3DB, for retrofitting and querying existing MBDs, such as GSDB, via OPM interfaces, and for constructing and experimenting with a federation consisting of GDB 6, GSDB, and Genbank.
The OPM toolkit is currently being extended with facilities that will support complex data types and external operations, such as 3D crystalographic data and 3D viewers, and will allow the construction of Electronic Notebooks for scientific applications. MBDs incorporating such complex data types will be implemented using combinations of conventional DBMSs and structured files, with OPM providing a seamless view of the underlying hybrid system. Interfaces for deploying MBDs in CORBA based environments are also developed.