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. 5.7, p. 562

Section 5.7.2.8. Publication

P. R. Strickland,a M. A. Hoylanda and B. McMahona*

aInternational Union of Crystallography, 5 Abbey Square, Chester CH1 2HU, England
Correspondence e-mail:  bm@iucr.org

5.7.2.8. Publication

| top | pdf |

When the final version of a CIF for Acta Cryst. C or E is approved, the article is ready for publication. Once more, the data fields required for the published article are extracted from the CIF and sorted. If the author has asked for additional items to be printed by using _publ_manuscript_incl_extra_item, these also are extracted. The result is transformed to a file suitable for processing by typesetting software. For Acta Cryst. C this was originally a [\hbox{\TeX}] file; now a further transformation generates an SGML file that conforms to the document type definition (DTD) common to all IUCr journals. This allows not only typesetting and printing, but also the generation of the HTML for the navigable online version of the article, and the extraction of metadata for building online tables of contents and for supplying to bibliographic databases.

The conventional published article then appears in a monthly issue. Each article is still similar in style to the type of structure report published in journals for decades, although tables of atomic positions and geometric data are not usually displayed now, since these data are so readily available from the online article.

The online version of the journal, however, presents a much more information-rich version of the article. Each article is generally available in the form of a PDF file, suitable for downloading and offline printing. There is also an HTML version of the same text, and this version has rich internal links that make it easy to scroll back and forth through the article, jump to specific sections and see figures in low-resolution thumbnail or high-resolution views. The reference list contains links to the articles that are cited. There may also be links to related records in chemical or crystal structure databases. The reader may also download the experimental data and any supplementary documents associated with the article. As mentioned above, for Acta Cryst. E a summary of the check report is also available.

Finally, the structural data may be downloaded directly in CIF format. The CIF is presented in two ways. If a reader follows one link in a web browser, the file is interpreted simply as a text file and appears as a simple listing in the browser window, from which it may be printed or saved to disk. However, if the reader follows the other link, the CIF is transmitted to the browser with a header declaring its MIME type (Freed & Borenstein, 1996[link]) as `chemical/x-cif'. This is one of several MIME types registered for particular presentations of chemistry-related content by Rzepa & Murray-Rust (1998[link]). The reader may then configure a web browser to respond in a specific way to content tagged with this MIME type; typically a helper application such as a molecular visualizer [e.g. Mercury (Bruno et al., 2002[link])] will be launched that allows three-dimensional visualization and manipulation of the molecular or crystal structure.

When an article has been published in Acta Cryst. C or E, the CIF is transferred to the relevant public structural databases. Thus, the transcription errors that used to cause so many problems for data harvesters are completely avoided and one of the initial goals of the CIF project is achieved: uncorrupted data transfer from diffractometer, through publication, to a final repository.

Because Acta Cryst. C and E handle almost exclusively the publication of structure reports, the editorial workflow based on CIF lends itself to a very high level of automation and the journals are produced efficiently and on short timescales. Routine refereeing of structures is made very easy by the provision of checking reports, and the universal use of e-mail and web file transfer means that production times can be very fast.

References

Bruno, I. J., Cole, J. C., Edgington, P. R., Kessler, M., Macrae, C. F., McCabe, P., Pearson, J. & Taylor, R. (2002). New software for searching the Cambridge Structural Database and visualizing crystal structures. Acta Cryst. B58, 389–397.Google Scholar
Freed, N. & Borenstein, N. (1996). Multipurpose Internet Mail Extensions (MIME) part two: media types. Internet Engineering Task Force. Request for comment 2046. http://www.ietf.org/rfc/rfc2046.txt Google Scholar
Rzepa, H. S., Murray-Rust, P. & Whitaker, B. J. (1998). The application of chemical Multipurpose Internet Mail Extensions (chemical MIME) internet standards to electronic mail and world-wide web information exchange. J. Chem. Inf. Comput. Sci. 38, 976–982.Google Scholar








































to end of page
to top of page