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. 3.2, pp. 112-114

Section 3.2.5. Publication

S. R. Hall,a* P. M. D. Fitzgeraldb and B. McMahonc

aSchool of Biomedical and Chemical Sciences, University of Western Australia, Crawley, 6009, Australia,bMerck Research Laboratories, Rahway, New Jersey, USA, and cInternational Union of Crystallography, 5 Abbey Square, Chester CH1 2HU, England
Correspondence e-mail:  syd@crystal.uwa.edu.au

3.2.5. Publication

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As an archival file format, CIF is well suited to the complete documentation of a structural study and the categories described in this section provide data items suitable for the generation of a fully documented report, either as an informal laboratory notebook document or as a formal published article.

3.2.5.1. Literature citations

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The categories describing literature citations are as follows:

CITATION group
 CITATION
 CITATION_AUTHOR
 CITATION_EDITOR

The entries in the CITATION category group provide a set of data items suitable for the structured recording of references to the literature. At present, they are designed for the storage and retrieval of information about journal articles and individual chapters in books. They do not currently cover conference proceedings, pamphlets, preprints, theses or other kinds of publication. Reference lists are usually requested by journals that accept articles in CIF format as a single text field in _publ_section_references, but the categories in the CITATION group may become more useful for storing citation lists in the future, especially if converters become available to and from other bibliographic formats such as EndNote and [{\rm Bib}\hbox{\TeX}].

Data items in these categories are as follows:

(a) CITATION [Scheme scheme72]

(b) CITATION_AUTHOR [Scheme scheme73]

(c) CITATION_EDITOR [Scheme scheme74]

The bullet ([\bullet]) indicates a category key. The arrow ([\rightarrow]) is a reference to a parent data item.

The CITATION category provides the bulk of the information about individual citations. _citation_id provides a link to the CITATION_AUTHOR and CITATION_EDITOR categories, where multiple authors, and, if appropriate, multiple editors are listed.

Example 3.2.5.1[link] shows how a fully populated citation list is structured across these categories.

Example 3.2.5.1. A structured bibliographic reference list.

[Scheme scheme75]

The authors of a cited reference are listed using items from the CITATION_AUTHOR category. The value of _citation_author_citation_id must match a value of _citation_id in the CITATION category, and this data item forms the link between the authors and the citations. _citation_author_ordinal is used to record the order in which the authors are listed.

The editors of a cited reference are listed using items from the CITATION_EDITOR category. The value of _citation_editor_citation_id must match a value of _citation_id in the CITATION category, and this data item forms the link between the editors and the citations. _citation_editor_ordinal is used to record the order in which the editors are listed.

3.2.5.2. Citation of software packages

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The single category describing software citations is as follows:

COMPUTING group
 COMPUTING

Data items in this category are as follows:

COMPUTING [Scheme scheme76]

The items in this category identify the software packages used for particular stages in a standard small-molecule crystallographic study. They may of course be used in other types of study as long as the description implied by the data name is relevant. The mmCIF dictionary provides a more general category, SOFTWARE, for the structured recording of programs used for a wider range of purposes.

3.2.5.3. Citation of related database entries

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The single category describing related database entries is as follows:

DATABASE group
 DATABASE

Data items in this category are as follows:

DATABASE [Scheme scheme77]

The _database_code_ items store the identifiers provided by specific databases for the structure described in the current data block. In the order given above, the databases they refer to are: Chemical Abstracts, the Cambridge Structural Database, the Inorganic Crystal Structure Database, the Metals Data File, the Crystal Data database of the National Institute of Standards and Technology (formerly the National Bureau of Standards), the Protein Data Bank, and the Powder Diffraction File of the International Centre for Diffraction Data.

The _database_code_depnum_ccdc_* items record deposition numbers assigned to files containing structural information archived by the Cambridge Crystallographic Data Centre (CCDC). The deposition numbers are as assigned by the CCDC itself (*_archive), by the Fachinformationszentrum Karlsruhe (*_fiz) or by a journal (*_journal). The item _database_CSD_history records the history of changes made by the CCDC and incorporated into the Cambridge Structural Database.

The _database_journal_ items store, respectively, the coden designator for journal titles of the American Society for Testing and Materials (ASTM), as given in the Chemical Source List maintained by the Chemical Abstracts Service, and the journal code used in the Cambridge Structural Database.

These specific items are regarded as appropriate for small-molecule and inorganic structures. The mmCIF dictionary includes a DATABASE_2 category, where an extensible data scheme allows additional database entries to be stored without requiring a separate data item for each new database reference.

3.2.5.4. Journal housekeeping, citation and indexing entries

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The categories used for journal housekeeping and indexing are as follows:

JOURNAL group
 JOURNAL
 JOURNAL_INDEX

The data items in the JOURNAL category group are concerned with the processing of an article for publication. They are used mainly by the staff of the editorial office of an academic journal and are of limited interest to the practising crystallographer. They are not defined explicitly in the core dictionary and are included here only for the sake of completeness.

(a) JOURNAL [Scheme scheme78]

(b) JOURNAL_INDEX [Scheme scheme79]

Of the data items in the JOURNAL category, the only ones that are likely to be of interest to users other than the journal staff are the items recording the bibliographic information upon publication, namely _journal_name_full, _journal_year, _journal_volume, _journal_page_first and _journal_page_last.

Data items in the JOURNAL_INDEX category allow terms to be embedded within a CIF that will be used for generating journal indexes. Example 3.2.5.2[link] shows how this is done; the possible values of _journal_index_type are defined by the journal and for Acta Crystallographica and other IUCr journals may be one of S (subject index), I (inorganic formula index), M (metal-organic formula index) or O (organic formula index).

Example 3.2.5.2. Markup of indexing terms.

[Scheme scheme80]

3.2.5.5. Contents of a publication

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Categories used to describe an article for publication and to include the text of an article are as follows:

PUBL group
 PUBL
 PUBL_AUTHOR
 PUBL_BODY
 PUBL_MANUSCRIPT_INCL

The items in the PUBL category group describe the text that an author adds to the experimental data in a CIF to create a full record of the structural study for publication.

Data items in these categories are as follows:

(a) PUBL [Scheme scheme81]

(b) PUBL_AUTHOR [Scheme scheme82]

(c) PUBL_BODY [Scheme scheme83]

(d) PUBL_MANUSCRIPT_INCL [Scheme scheme84]

The data items in the PUBL category represent non-looped components of the published article, varying from the article title to the complete text of the article. Some journals such as Acta Crystallographica require specific section headers in articles, for which data items (e.g. _publ_section_comment) are provided. An alternative approach is to use the general items in this list for the article title, abstract, reference list etc. and build the individual sections of text using the items in the PUBL_BODY category.

The CIF syntax restrictions that permit only printable ASCII characters (Chapter 2.2[link] ) mean that authors cannot simply cut and paste text produced by commercial word-processing programs into a CIF. This might be inconvenient for the author, but while commercial word-processing programs are often convenient to use, they use proprietary and often poorly documented formats. For an archived CIF to remain readable in the long term, the use of transparent text representations, using open and well documented markup systems such as XML or [\hbox{\TeX}], is preferred.

The authors of an article are listed separately using items in the PUBL_AUTHOR category. The entry for each author can be annotated, for example to add text that would appear as a footnote to the author's name in the published article.

The PUBL_BODY category allows the body of an article to be more highly structured than _publ_manuscript_text does. It may be used for articles that include structural data but are less formally structured than required by Acta Crystallographica Section C or Acta Crystallographica Section E.

Journals like Acta Crystallographica Section C may have a list of CIF data items that will normally be published. If an author wishes to include additional data items, they can be specified using the _PUBL_MANUSCRIPT_INCL category. Since the values of _publ_manuscript_incl_extra_item are data names, they must be placed in quotes, as in Example 3.2.5.3[link], for them to be parsed correctly.

Example 3.2.5.3. Request to add material for publication to a journal's standard list.

[Scheme scheme85]

Further information on the use of the data items in the PUBL category group may be found in Section 5.7.2.[link]








































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