Section 5.7.3.2. CIF and XML

XML is a specific concrete implementation of SGML suitable for generation of online browsable content. Mature style transformation mechanisms for XML exist and others are under active development.

Section 5.3.8.2.1 describes one transformation to XML in the biological structures field, designed primarily for database interchange rather than publication. This transformation preserves the underlying data model of an mmCIF very closely, and one might anticipate similar XML transformations for small-molecule CIF applications and for publications. It is even possible that the XML transformations referred to in Chapter 5.3 could be used for publishing articles if suitable style transformations are developed, but this has not been tested yet.

One difficulty with a simple CIF-to-XML transformation is that it could be easily adapted to the publication of structure reports in dedicated journals, but would not necessarily be compatible with other XML implementations developed by an unspecialized publishing house. This could be avoided by the registration of an XML name space covering transformed CIF data and the production of portable stylesheet transformations that could be adopted and modified to meet the requirements of different publishing houses. As yet, we know of no initiatives in this direction.

XML name spaces have been registered to safeguard the development of subject-specific methods of representation as part of a project by the International Union of Pure and Applied Chemistry (Becker, 2001). One markup language that falls within the scope of this project is Chemical Markup Language (CML) (Murray-Rust & Rzepa, 1999, 2001).

Further discussions of the relationship between CIF and XML representations and a proposal for extensions to certain CIF data values to accommodate the wider range of data structures permitted in XML are given by Bernstein (2000).