2.1. Specification of the STAR File
S. R. Hall and N. Spadaccini
Abstract
The general concepts and requirements of a universal exchange file are introduced in this chapter. The Self-defining Text Archive and Retrieval (STAR) File was designed to meet the requirements for a universal data-exchange mechanism, and it is the format widely used in structural science to exchange and archive numerical and text data.
The STAR File structure is simple. Discrete data values, always represented by ASCII character strings, are identified by distinguishable tags. A file is partitioned into one or more blocks of data. Within each such block, one or more subsidiary blocks (known as save frames) may encapsulate a set of data items. In each block, a given tag may appear once only, but may index a single data value or a set of looped values. Loops of related items may be combined in tabular structures. Global blocks may occur that establish data values inherited by succeeding data blocks.
This chapter describes the STAR File syntax and scoping rules in detail, and provides a formal grammar in extended Backus-Naur form.
Links
Supplementary documents
- Backus-Naur form of the STAR syntax and grammar (HTML format)
- Backus-Naur form of the STAR syntax and grammar (plain text file with Unix-style line endings)
References
Allen, F. H., Barnard, J. M.,
Cook, A. P. F. & Hall, S. R. (1995). The Molecular
Information File (MIF): core specifications of a new standard format
for chemical data. J. Chem. Inf. Comput. Sci. 35,
412-427.
Hall, S. R. (1991). The STAR file: a new
format for electronic data transfer and archiving.
J. Chem. Inf. Comput. Sci. 31, 326-333.
Hall, S. R., Allen, F. H. &
Brown, I. D. (1991). The Crystallographic Information File
(CIF): a new standard archive file for crystallography.
Acta Cryst. A47, 655-685.
See also
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HTML version
(http://www.iucr.org/iucr-top/cif/standard/cifstd1.html).
Hall, S. R. & Cook, A. P. F.
(1995). STAR Dictionary Definition Language: initial
specification. J. Chem. Inf. Comput. Sci. 35,
819-825.
Hall, S. R. & Sievers, R. (1990).
QUASAR: CIF syntax checking and file manipulation tool.
ftp://ftp.iucr.org/pub/quasar.
See also Hall, S. R. & Sievers, R. (1996). CIF
applications. I. QUASAR: for extracting data from a CIF.
J. Appl. Cryst. 26, 469-473.
Hall, S. R. & Spadaccini, N. (1994).
The STAR File: detailed specifications. J. Chem. Inf. Comput.
Sci. 34, 505-508.
ISO (2002). ISO/IEC 8824-1. Abstract Syntax
Notation One (ASN.1). Specification of basic notation.
Geneva: International Organization for Standardization.
See also
http://asn1.elibel.tm.fr/en/index.htm
McCarthy, J. L. (1990). Data interchange standards for biotechnology: issues and alternatives. National Center for Biotechnical Information Report. NIH/DOE.
McLennon, B. J. (1983). Principles of programming languages, design, evaluation and implementation. New York: Holt, Rinehart and Winston.
Spadaccini, N., Hall, S. R. &
Castleden, I. R. (2000). Relational expressions in STAR File
dictionaries. J. Chem. Inf. Comput. Sci. 40,
1289-1301.
Westbrook, J. D. & Hall, S. R. (1995). A Dictionary Language for Macromolecular Structure. DDL 2.1.1. http://ndbserver.rutgers.edu/mmcif/ddl.