An ontology driven architecture for derived representations of macromolecular structure

Douglas S Greer; John D Westbrook; Philip E Bourne

doi:10.1093/bioinformatics/18.9.1280

An ontology driven architecture for derived representations of macromolecular structure

Bioinformatics. 2002 Sep;18(9):1280-1. doi: 10.1093/bioinformatics/18.9.1280.

Authors

Douglas S Greer¹, John D Westbrook, Philip E Bourne

Affiliation

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. dsg@sdsc.edu

PMID: 12217927
DOI: 10.1093/bioinformatics/18.9.1280

Abstract

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@sdsc.edu

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Database Management Systems*
Databases, Factual*
Information Storage and Retrieval / methods*
Internet
Local Area Networks*
Macromolecular Substances*
Molecular Structure*

Substances

Macromolecular Substances