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. 84

Section 3.1.7.3. Construction of data names

B. McMahona*

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

3.1.7.3. Construction of data names

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Since a dictionary definition contains all the machine-readable attributes necessary for validating the contents of a data field, the data name itself may be an arbitrary tag, devoid of semantic content. However, while dictionary-driven access to a CIF is useful in many cases, there are circumstances where it is useful to browse the file. It is therefore helpful to construct a data name in a way that gives a good indication of the quantity described. From the beginning, CIF data names have been constructed from self-descriptive components in an order that reflects the hierarchical relationship of the component ideas, from highest (most general) level to lowest (most specific) level when read from left to right.

In a typical example from the core CIF dictionary, the data name _atom_site_type_symbol defines a code (symbol) indicating the chemical nature (type) of the occupant of a location in the crystal lattice (atom_site). The equivalent data name from the mmCIF dictionary, _atom_site.type_symbol, explicitly separates the category to which the data name belongs from its more specific qualifiers by using a full stop (.) instead of an underscore (_). While this use of a full stop is mandated in DDL2 dictionaries, it should nevertheless be considered a convenience, since the category membership is explicitly listed in the dictionary definition frame for every data name.

However, it may not always be easy to establish the best order of components when constructing a new data name. In the JOURNAL category, there was initially some uncertainty about whether to associate the telephone numbers of different contact persons by appending codes such as _coeditor and _techeditor to a common base name. In the end, the order of components was reversed to give names like _journal_coeditor_phone and _journal_techeditor_phone. Examining the JOURNAL category in the core CIF dictionary will show why this was done. Similarly, the extension of geometry categories to include details of hydrogen bonding went through a stage of discussing adding new data names to the existing categories, but with suffixes indicating that the components were participating in hydrogen bonding, before it was decided that a completely new category for describing all elements of a hydrogen bond was justified. These examples show that the correct ordering of components within a data name is closely related to the perceived classification of data names by category and subcategory.

Sometimes it is useful to differentiate alternative data items by appending a suffix to a root data name. For example, the core dictionary defines several data names for recording the reference codes associated with a data block by different databases: _database_code_CAS, _database_code_CSD etc. This is convenient where there are two or three alternatives, but becomes unwieldy when the number of possibilities increases, because new data names need to be defined for each new alternative case. A better solution is to have a single base name and a companion data item that defines which of the available alternatives the base item refers to. The mmCIF dictionary follows this principle: the category DATABASE_2 contains two data names, _database_2.database_code (the value of which is an assigned database code) and _database_2.database_id (the value of which identifies which of the possible databases assigned the code) (Fig. 3.1.7.1[link]).

[Figure 3.1.7.1]

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Alternative quantities described (a) by data-name extension (core dictionary) or (b) by paired data names (mmCIF dictionary).

Note the distinction between a data name constructed with a suffix indicating a particular database, and a data name which incorporates a prefix registered for the private use of a database. The data name _database_code_PDB is a public data name specifying an entry in the Protein Data Bank, while _pdb_database_code is a private data name used for some internal purpose by the Protein Data Bank (see Section 3.1.8.2[link]).








































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