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. 2.2, p. 24

Section 2.2.5.3. Extended data typing: content type and encoding

S. R. Halla* and J. D. Westbrookb

2.2.5.3. Extended data typing: content type and encoding

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The initial implementation of CIF assumed that most character strings would represent identifiers or terse descriptions or comments, and that the correct behaviour of the majority of CIF applications would be simply to store these in computer memory or retrieve them verbatim. Only a few data values were foreseen as having extended content that might need special handling. For example, the complete text of a manuscript was envisaged as being included in the field _publ_manuscript_processed. The handling of this field (its extraction and typesetting) would be left to unspecified external agents, although some clue as to the provenance of the contents of that field (and thus their appropriate handling) would be given by _publ_manuscript_creation.

However, the evolution of CIF applications has required that some element of typographic markup be permitted in a growing number of data values, and future applications may be envisaged in which graphical images, virtual-reality models, spreadsheet tables or other complex objects are embedded as the values of specific data items. Since it will not be possible to write general-purpose CIF applications capable of handling all such embedded content, techniques will need to be developed for transferring each such field to a specialized but separate content handler. In the meantime, the rather ad hoc conventions for introducing typographic markup available at present are described in Sections 2.2.7.4.13[link]–17. It is hoped that in the future different types of such markup may be permitted so long as the data values affected can be tagged with an indication of their content type that allows the appropriate content handlers to be invoked.

It has also been necessary to allow native binary objects to be incorporated as CIF data values. This was done to support the storage of the large arrays of image data obtained from area detectors. Since the CIF character set is based on printable ASCII characters only, encodings including compression have been developed to permit interconversion between ASCII and binary representations of such data (see Chapter 2.3[link] ).

Nowadays, arbitrary embedded objects may be transported in web pages via the http protocol (Fielding et al., 1999[link]) or as attachments to email messages structured according to the MIME protocols (e.g. Freed & Borenstein, 1996[link]). Identification of encoding techniques and hooks to invoke suitable handlers are carried in the relevant Content-Type and Content-Encoding http or MIME headers. It is suggested that this may form the basis of suitable tagging of content types and encoding for future CIF development.

A candidate for a CIF-specific encoding protocol is the special convention introduced with CIF version 1.1 to interconvert long lines of text between the new and old length limits (Section 2.2.7.4.11[link]). This is an encoding in the sense that it is a device designed to retain any semantic content implicit in textual layout, while conforming to slightly different rules of syntax. It is designed to enable CIFs written to the longer line-length specification to be transformed so that they can still be handled by older software. Since the object of the exercise is to manage legacy applications, it is likely that the interconversion will be done through external applications, or filters, designed specifically for the purpose. Such a conversion filter is conceptually the same as a filter to convert a binary file into an ASCII base-64 encoding, for example.

References

Fielding, R., Gettys, J., Mogul, J., Frystyk, H., Masinter, L., Leach, P. & Berners-Lee, T. (1999). Hypertext Transfer Protocol – HTTP/1.1. RFC 2616. Network Working Group. http://www.w3.org/Protocols/rfc2616/rfc2616.html .
Freed, N. & Borenstein, N. (1996). Multipurpose Internet Mail Extensions (MIME) Part two: media types. RFC 2046. Network Working Group. http://www.ietf.org/rfc/rfc2046.txt .








































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