International
Tables for
Crystallography
Volume G
Definition and exchange of crystallographic data
Edited by S. R. Hall and B. McMahon

International Tables for Crystallography (2006). Vol. G, ch. 1.1, p. 7

Section 1.1.8. Diversification: the Molecular Information File and dictionary definition language

S. R. Halla* and B. McMahonb

aSchool of Biomedical and Chemical Sciences, University of Western Australia, Crawley, Perth, WA 6009, Australia, and bInternational Union of Crystallography, 5 Abbey Square, Chester CH1 2HU, England
Correspondence e-mail:  syd@crystal.uwa.edu.au

1.1.8. Diversification: the Molecular Information File and dictionary definition language

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While the primary thrust of these activities was the development of an exchange mechanism for crystal-structure reports, there was also interest in enriching the description of the chemical properties and behaviour of the compounds under study. Some work was therefore done to broaden the descriptions of bond order that were present in rudimentary form in the core CIF dictionary and to develop more detailed two-dimensional graphical representations of chemical molecules. The result of this work was the Molecular Information File (MIF), described in Chapter 2.4[link] . As with CIF, the specific data items required for MIF were defined in a dictionary.

This work has extended the STAR File approach into chemistry. It is envisaged that later modules could describe spectroscopic data, reaction schemes and much more. Particular requirements of chemical structural databases are the need to query for generic structures, and the need to allow for the labelling and comparison of libraries of substructural components. Both requirements can be met by features of the STAR File, but they are features omitted from CIF. In practice, therefore, data files in MIF format cannot be readily accessed by most crystallographic applications, and the format is at present little used by crystallographers.

An important outcome of the work on MIF was the recognition that attributes of the data items needed for a particular application can be recorded using the same formalism as the data files themselves. This gave rise to the idea of a dictionary definition language (DDL), a set of tags for describing the names and attributes of data items. The dictionaries (the collections of data names for CIF and MIF applications) could then be constructed as STAR Files themselves, with the immediate result that software written to parse data files could equally easily parse the associated dictionaries. Now it became feasible to build into applications the ability to validate data by dynamically reading and interpreting the properties associated with a data tag in an accompanying dictionary.

The idea of a DDL was proposed by Tony Cook during early discussions on MIF and was adopted while the original CIF paper (Hall et al., 1991[link]) was in the press. The original core CIF dictionary was therefore produced with an early version of a DDL that was never fully documented (Fig. 1.1.8.1[link]). Building on early experience with the core dictionary and the technical evolution of MIF, Hall & Cook (1995[link]) worked through several revisions before publishing DDL version 1.4, the stable version described in Chapter 2.5[link] of this volume. Because of the circumstances in which it was developed, this dictionary definition language is able to accommodate both the flat-file quasi-relational structure of CIF and the more hierarchical multiple-looped data model of MIF.

[Figure 1.1.8.1]

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Informal DDL used in the initial version of the core CIF dictionary (now superseded by DDL1.4).

References

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.
Hall, S. R. & Cook, A. P. F. (1995). STAR dictionary definition language: initial specification. J. Chem. Inf. Comput. Sci. 35, 819–825.








































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