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, pp. 81-83

Section 3.1.6.5. Data-item definitions

B. McMahona*

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

3.1.6.5. Data-item definitions

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The bulk of a DDL2 data dictionary comprises the save frames that include descriptions of the meaning and properties of individual data names.

Unlike DDL1 dictionaries, where the definitions of several data names may be contained in a single data block (most commonly for a set of items that form a logical irreducible set), save frames in DDL2 dictionaries each contain the definition for a single addressable concept.

For example, the three Miller index components of a diffraction reflection ( _diffrn_refln_index_h, _diffrn_refln_index_k, _diffrn_refln_index_l that are described in the DDL1 core CIF dictionary in the data block data_diffrn_refln_) are described in a DDL2 dictionary in three separate save frames, save_ _diffrn_refln.index_h, save_ _diffrn_refln.index_k and save_ _diffrn_refln.index_l. In the DDL2 formalism, the intimate relationship between these three components is expressed through the common _item_sub_category.id value of miller_index and the mutual reference of the other Miller-index components by the _item_dependent.dependent_name entries in each separate save frame.

An apparent exception to this general rule is the case of save frames defining an item, often a category key, that is an identifier common to several categories. In this case, the save frame defining the `parent' identifier implicitly defines the complete property set of each child identifier. For completeness, the respective child identifiers are each declared in their own save frames, but these act only as back references to the parent definition. This is explained more completely in Section 3.1.6.5.1[link] below.

3.1.6.5.1. Inheritance of identifiers

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Example 3.1.6.6[link] is from an mmCIF of two related categories that describe characteristics of an active site in a macromolecular complex. The sites are described in general terms with a label and textual description in the STRUCT_SITE category (the first looped list in the example). Details of how each site is generated from a list of structural features form the STRUCT_SITE_GEN category (second loop or table).

Example 3.1.6.6. Illustration of parent/child relationships between identifiers in related categories.

[Scheme scheme15]

It is clear that each instance of the data item _struct_site_gen.site_id in the second table must have one of the values listed as _struct_site.id in the first loop, because it is the purpose of these identifiers to relate the two sets of data: they are the glue between the two separate tables and must have the same values to ensure the referential integrity of the data set (that is, the consistency and completeness of cross-references between tables). Within a group of related categories like this, it is normal to consider one as the `parent' and the others as `children'.

Because all such linking data items must have compatible attributes, it is conventional in DDL2 dictionaries to define all the attributes in a single location, namely the save frame which hosts the definition of the `parent' data item. In early drafts of DDL2 dictionaries, the `children' were not referenced at all in separate save frames; software validating a data file against a dictionary was required to obtain all information about a child identifier from the contents of the save frame defining the parent. However, subsequent drafts introduced a minimal save frame for the children to accommodate dictionary browsers that depended on the existence of a separate definition block for each individual data item.

Consequently, the definition blocks in current DDL2 dictionaries conform to the structure in Example 3.1.6.7[link], which refers to the simple STRUCT_SITE example used above.

Example 3.1.6.7. A definition of an identifier which is parent to identifiers in other categories.

[Scheme scheme16]

Note that the dependent data names are listed twice: once in the loop that declares their _item.name values and the categories with which they are associated; and again in a loop that makes the direction of the relationship explicit. A parent data item may have several children, but each child can have only a single parent (i.e. related data name whose value may be checked for referential integrity). Note also that each listed item has an _item.mandatory_code value of yes: because they are identifiers which link categories, they must be present in a table to allow the relationships between data items in different tables to be traced.

Other than the specific description text field, any declared attributes (in this example only the data type) have a common value across the set of related identifiers.

As mentioned above, it is not formally necessary to have a separate save frame for the individual children; but it is conventional to have such individual save frames containing minimal definitions that serve as back references to the primary information in the parent frame. These also provide somewhere for the specific text definitions for the children to be stored. The definition frame for _struct_site_gen.id is shown in Example 3.1.6.8[link].

Example 3.1.6.8. Definition of a child identifier.

[Scheme scheme17]

3.1.6.5.2. Definitions of single quantities

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While it is important to ensure the referential integrity of the data in a CIF through proper book-keeping of links between tables, the crystallographer who wishes to create or extend a CIF dictionary will be more interested in the definitions of data items that refer to real physical quantities, the properties of a crystal or the details of the experiment. The DDL2 formalism makes it easy to create a detailed machine-readable listing of the attributes of such data.

Example 3.1.6.9[link] parallels the example chosen for DDL1 dictionaries of the ambient temperature during the experiment.

Example 3.1.6.9. DDL2 definition of a physical quantity.

[Scheme scheme18]

In the definition save frame, the category is specifically listed (although it is deducible from the DDL2 convention of separating the category name from the rest of the name by a full stop in the data name). The data type is specified as a floating-point number. (In the core dictionary there are fewer data types and the fact that the value may be a real rather than integer number must be inferred from the declared range.) The range of values is also specified with separate maximum and minimum values (unlike in DDL1 dictionaries, which give a single character string that must be parsed into its component minimum and maximum values). The assignment of the same value to a maximum and a minimum means that the absolute value is permitted; without the repeated `0.0' line the range in this example would be constrained to be positive definite; the equal value of 0.0 for maximum and minimum means that it may be identically zero.

The _item_units.code value must be one of the entries in the units table for the dictionary and can thus be converted into other units as specified in the units conversion table.

The aliases entries identify the corresponding quantity defined in the DDL1 core dictionary.








































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