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. 3.1, p. 74

Section 3.1.2. Informal definition procedures

B. McMahona*

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

3.1.2. Informal definition procedures

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Before considering the techniques for defining data items in standard globally adopted dictionaries, it is important to discuss the techniques for including information that is only of local interest in a way that does not conflict with public data names.

An author of a CIF is free to include data names for local use (i.e. names not intended for common use across the community). However, such local data names must not conflict with those defined in public dictionaries, since the data name alone identifies the meaning that one must attach to an associated data value. Some protocols and conventions exist to prevent conflict in data names when the local data name is invented or subsequently, when later public dictionaries are released.

An author may also define local data names in some completely informal manner; that is, there is no obligation to construct an attribute table in an external file that conforms to the style of the public dictionaries. Nevertheless, there are clear advantages to doing so: the author will benefit from standard software tools that validate data against dictionaries and the data names are more easily exported to the public domain if they subsequently become relevant to a wider community. In the following, it is assumed that the author of a new data name wishes to define fully its attributes in an appropriate standard dictionary formalism.

3.1.2.1. The _[local]_ prefix

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The string _[local]_ is reserved as a prefix to identify data names that do not appear in any public dictionary. (The left and right square brackets are included in this label.) Hence an author may construct private data names according to one of the following models, secure in the knowledge that the name will not appear in any global dictionary. With DDL1, a private data name will always have the form _[local]_private_data_name, while with DDL2 the forms _[local]_new_category_name.private_data_name and _existing_category_name.[local]_private_data_name may be used. The first DDL2 form is used for private data names in a category not already defined by a public dictionary; the second form permits the addition of local data names to an existing category. Note that the initial underscore character is dropped in the second DDL2 form.

While this convention guarantees that the new data name will not conflict with a public one, it cannot guarantee that it will not conflict with a local data name created by another author. Therefore these data names are appropriate only for testing purposes and not for release in data files that may be used by others.

3.1.2.2. Reserved prefixes

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To guarantee that locally devised data names may be placed without name conflict in interchange data files, authors may register a reserved character string for their sole use. As with the special prefix _[local]_ discussed in Section 3.1.2.1[link], the author's reserved prefix is simply an underscore-bounded string within the data name (i.e. it may not itself include an underscore character). For DDL1 applications it must be the first component of the data name; for DDL2 applications it forms the first component of the data name if describing data names in a category not defined in the official dictionaries; or the first component after the full stop (category delimiter) if the local data name is an extension to an existing category.

Prefixes may be registered online through a web form at http://www.iucr.org/iucr-top/cif/spec/reserved.html . Table 3.1.2.1[link] gives a list of prefixes registered as of March 2005; this list will of course go out of date, but a current list will be maintained on the web at the address above.

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Reserved prefixes for private CIF data names

StringReserved for the use of
anbf Australian National Beamline Facility
asd Active Site Database
B+S Software developers Bernstein + Sons
ccdc Cambridge Crystallographic Data Centre
CCP4 CCP4 program system
cgraph Oxford Cryosystems Crystallographica package
cifdic Register of CIF dictionaries
crystmol CrystMol package
csd Cambridge Structural Database
ebi European Bioinformatics Institute
edchem Edinburgh University Chemistry Department
gsas GSAS powder refinement system
gsk Glaxo Smith Kline
iims EBI project on integration of information about macromolecular structure
iucr IUCr journal use
mdb Model Database (Glaxo)
msd EBI Molecular Structure Database Group
ndb Nucleic Acids Database Project, Rutgers University
oxford CRYSTALS package, University of Oxford
parvati Validation and statistical summaries from PARVATI validation server
pdb Protein Data Bank
pdbx Protein Data Bank exchange dictionary
pdb2cif Additions to mmCIF used by program pdb2cif
rcsb Research Collaboratory for Structural Bioinformatics
shelx SHELXL solution and refinement programs
vrf Validation reply form (IUCr/Acta Crystallographica use)
wdc Entries in the World Directory of Crystallographers
xtal Xtal program system

An example of a data name incorporating a reserved prefix is the listing of a protein amino-acid sequence recorded temporarily by the Protein Data Bank before a protein structure is released, _pdbx_prerelease_seq.seq_one_letter_code.

3.1.2.3. Name spaces

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The allocation of special prefixes as in Sections 3.1.2.1[link] and 3.1.2.2[link] above is a basic form of name-space allocation, because it gives authors the freedom to reproduce portions of otherwise standard data names within their own private constructions. This raises the wider question of whether a complete formalism for name-space allocation is needed. That is, the same data name might appear with different meanings in different files, provided it was clear which of the alternative definitions must be used in each case. For now, the decision has been taken not to permit the use of the same data names with different meanings in different contexts. This is to enforce uniformity of definition across the whole field of crystallography as far as is possible. This policy might be reviewed in the future if similar formalisms to CIF are created in related disciplines.








































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