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. 5.2, p. 488

Section 5.2.1. Introduction

N. Spadaccini,a* S. R. Hallb and B. McMahonc

aSchool of Computer Science and Software Engineering, University of Western Australia, 35 Stirling Highway, Crawley, Perth, WA 6009, Australia,bSchool of Biomedical and Chemical Sciences, University of Western Australia, Crawley, Perth, WA 6009, Australia, and cInternational Union of Crystallography, 5 Abbey Square, Chester CH1 2HU, England
Correspondence e-mail:  nick@csse.uwa.edu.au

5.2.1. Introduction

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The STAR File, described in Chapter 2.1[link] , has a simple format intended to allow the flexible and extensible representation of data without regard to specific data models. In crystallography and related disciplines, the restricted format chosen for the Crystallographic Information File (CIF, Chapter 2.2[link] ) and Crystallographic Binary File (CBF, Chapter 2.3[link] ) lends itself to rather flat data models. In particular, the relationships between data items enforced through DDL2 dictionaries in applications such as mmCIF (Chapter 3.6[link] ) are essentially equivalent to the data structures and relationships of a relational database. Of course, properly normalized relational tables can represent a hierarchy of structure, although this may not be an efficient representation.

There are other applications, such as the molecular information file (MIF, Chapter 2.4[link] , that make use of additional features of the STAR File, such as multiple-level loop structures, global variable scoping and data-instance encapsulation in save frames. These applications may more efficiently represent certain hierarchical or object-oriented data models.

While particular applications require software tools tailored to their specific purposes, it is helpful to have programs or libraries capable of manipulating arbitrary STAR File data, relying solely on the syntax rules and format of the STAR File and taking no account of the semantic content of the included data.

In this chapter, the stand-alone program Star_Base is described in detail. This program uses a local query language to demonstrate the ability to retrieve or re-order data with their associated context. There is also a brief review of Star.vim and StarMarkUp, applications for editing and browsing STAR Files. The chapter concludes by reviewing a number of object classes and libraries for a variety of STAR and generalized CIF applications: prototypical approaches OOSTAR and CIF++, CIFOBJ and starlib used by major macromolecular data repositories, and the document-object model package StarDOM.








































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