Bioinformatics Vol. 16 no. 2 2000
Pages 159-168
© 2000 Oxford University Press
STAR/mmCIF: An ontology for macromolecular structure
1 Rutgers, The State University of New
Jersey, Department of Chemistry, 610 Taylor Road, Piscataway, NJ
08854-8087, USA,
2 San Diego Supercomputer Center and
Department of Pharmacology, University of California, San Diego,
9500 Gilman Drive, La Jolla CA 92093-0505, USAand The Burnham
Institute, 10901 N. Torrey Pines Road, La Jolla CA 92037, USA
To whom correspondence should be addressed.
Motivation: Crystallographers were motivated 10 years ago to develop a simple and consistent data representation for the exchange and archiving of data associated with the crystallographic experiment and the final structure. As this process evolved (and the data grew at near exponential rates) came the recognition that this representation should also facilitate the automated management of the data and, with the aid of additional software for verification and validation, provide improved consistency and accuracy and hence improved scientific inquiry. This realization led to a new Dictionary Definition Language (DDL) and an extensive dictionary based on this DDL for describing macromolecular structure. In broad terms this could be considered an ontology. An important feature in the development of the ontology was the endorsement and ongoing maintenance and support of the International Union of Crystallography (IUCr). While the description of macromolecular structure and the x-ray crystallographic experiment used to derive it represent explicit data, the ontology is extensible and applicable to other less well- characterized data domains.
Results: Details of the DDL, the dictionaries that have been developed, and software for reading and using this ontology are presented.
Availability: Extensive documentation, software tools and the DDL and dictionaries are available from http://ndbserver.rutgers.edu/mmcifand associated mirror sites.
Contact: Bourne: bourne{at}sdsc.eduand Westbrook: jwest{at}rcsb.rutgers.edu
Received on July 7, 1999
; revised on August 16, 1999
; accepted on September 14, 1999
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