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Bioinformatics Vol. 18 no. 9 2002
Pages 1280-1281
© 2002 Oxford University Press

Applications Note

An ontology driven architecture for derived representations of macromolecular structure

Douglas S. Greer 1,*, John D. Westbrook 2 and Philip E. Bourne 1

1 The Research Collaboratory for Structural Bioinformatics at the San Diego Supercomputer Center, 9500 Gilman Drive, University of California, San Diego, La Jolla CA 92093-0505, USA
2 at Rutgers, the State University of New Jersey, Department of Chemistry and Chemical Biology, 610 Taylor Road, Piscataway, NJ 08854-8087, USA

Received on January 23, 2002 ; revised on February 20, 2002 ; accepted on March 25, 2002

Summary: An object metamodel based on a standard scientific ontology has been developed and used to generate a CORBA interface, an SQL schema and an XML representation for macromolecular structure (MMS) data. In addition to the interface and schema definitions, the metamodel was also used to generate the core elements of a CORBA reference server and a JDBC database loader. The Java source code which implements this metamodel, the CORBA server, database loader and XML converter along with detailed documentation and code examples are available as part of the OpenMMS toolkit.

Availability: http://openmms.sdsc.edu

Contact: dsg{at}sdsc.edu

* To whom correspondence should be addressed.


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