On Tuesday, February 27, 2001, the Board of Directors of the Object Management Group (OMG) voted to adopt the Common Object Request Broker Architecture (CORBA) Macromolecular Structure Specification. This specification opens the door to seamless and more specific access to PDB data. It will provide a standard application programming interface (API) that allows direct access by remote programs to the binary data structures of the PDB. Designed in collaboration with the International Union of Crystallography (IUCr), the new standard is based on the Macromolecular Crystallographic Information File (mmCIF) data representation**. Unlike current access in which users are required to retrieve and parse complete PDB files, an implementation of this CORBA API will allow applications to retrieve a single data item from a remote PDB server and import it for use in a local application.
CORBA provides a platform- and programming language-neutral mechanism for specifying distributed, object-oriented interfaces. The OMG, which oversees the development of CORBA and several other open standards for object-oriented computing, also charters groups such as the Life Sciences Research (LSR) Task Force for work in specific application domains. In addition to macromolecular structure, the LSR has also defined or is currently working on interface specifications in areas such as sequence analysis, gene expression, and laboratory equipment control. Collectively, these specifications should provide a robust framework for the development and integration of key data resources required by the structural biology community.
This initiative was led by Dr. Douglas Greer of the San Diego Supercomputer Center (SDSC). Dr. Greer is also the chair of the Macromolecular Structure Finalization Task Force (FTF), a newly created entity within the OMG with the charter of making any necessary changes to the specification necessary for implementation. A reference implementation with source code is expected to be publicly available from the PDB in the next year.
Additional information is available at the following sites:
OMG and LSR: http://www.omg.org/
** P.E. Bourne, H.M. Berman, B. McMahon, K. Watenpaugh, J. Westbrook, and P.M.D. Fitzgerald (1997): The Macromolecular CIF Dictionary. Methods in Enzymology 277, pp. 571-590.
The RCSB PDB (citation) is managed by two members of the Research Collaboratory for Structural Bioinformatics:
RCSB PDB is a member of the
The RCSB PDB is funded by a grant (DBI-1338415) from the
National Science Foundation, the
National Institutes of Health, and the
US Department of Energy.