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. 2.5, pp. 57-60

Section 2.5.6. DDL1 attribute descriptions

S. R. Halla* and A. P. F. Cookb

aSchool of Biomedical and Chemical Sciences, University of Western Australia, Crawley, Perth, WA 6009, Australia, and bBCI Ltd, 46 Uppergate Road, Stannington, Sheffield S6 6BX, England
Correspondence e-mail:  syd@crystal.uwa.edu.au

2.5.6. DDL1 attribute descriptions

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This section provides an overview of the different attributes that make up the core data dictionary language DDL1. A more detailed description of attributes is given in the DDL1 dictionary in Chapter 4.9[link] . In this dictionary the attributes are used to define themselves!

DDL1 attributes are most easily understood when considered in groups with common descriptive functions. There are five basic functional groups of attributes, which perform the definition tasks of identifying, describing, typing, relating and registering data items.

2.5.6.1. Identification attributes

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Establishing the identity of a data item is a primary function of a dictionary. In a data instantiation each item is recognized by a unique code, known as its data name or tag. This tag provides the most fundamental level of data validation.

The `identification' attribute in DDL1 dictionaries is _name, and appears in a definition as [Scheme scheme1]

The tag of the defined item is the value of _name and, because it starts with an underscore, it must always be bounded by quotes to prevent it from being interpreted as the start of another tag–value pair. If there is more than one data item in a definition, as in the case of an irreducible set of items, the data names are entered as a list starting with the statement [Scheme scheme2] (see the example in Fig. 2.5.5.8[link]).

The presence of the identification attribute _name in a definition is mandatory. Its value, the name of the defined items, provides for spelling validation. Note that if a data item in a CIF is not defined in a dictionary the CIF is still valid, although CIF parsers that employ dictionaries as part of the scanning process usually flag undefined items. The accepted practice to date is that undefined data are largely ignored by a dictionary validation process. In contrast, the need for certain defined items to be present in CIF data can be crucial because of list dependencies. The attributes that specify data relationships and links are considered in Section 2.5.6.4[link].

2.5.6.2. Descriptive attributes

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Three DDL1 attributes are used to provide text descriptions of a defined data item. These are present in a dictionary for human readability, browser software or for the production of text dictionaries such as those in Part 4. This group of attributes is not machine interpretable. [Scheme scheme3] The _definition attribute provides a text description and as such is the primary semantic content in a defined data item. It may also be used to provide supplementary information about other machine-parsable attributes in the definition (see the definition in Fig. 2.5.5.3[link]). The attributes _example and _example_detail are used to show typical instantiations of the defined item, as also shown in Fig. 2.5.5.6[link].

2.5.6.3. Typing attributes

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This class of attributes is used to specify the fundamental characteristics of data items and how they may be instantiated. These attributes are machine-parsable and of particular importance in the validation of CIF data. They are [Scheme scheme4] Enumeration attributes are used to specify restricted values, or `states', of a data item (see the example in Fig. 2.5.5.9[link]). They are not applicable in a definition of an item with unrestricted values. The attributes _enumeration and _enumeration_detail are used in definitions to specify permitted states and their descriptions. For instance, in a definition of atomic element symbols these attributes would be used to list the IUPAC `element symbols' and `element names'. When a data item is restricted to an ordinal set of values, the attribute _enumeration_range is used to define the minimum and maximum values of the logical sequence in the format <min>:<max> The attribute _enumeration_default may be used to specify the default value if an item is not present in a data instantiation.

List attributes specify how, and when, data items are used in a (looped) list. The attribute _list has a value of yes if a defined item must be in a list, and no if it must not. A value of both allows for both uses. The attribute _list_level specifies the nesting level of a list defined item. Only level 1 data are allowed in a CIF (see Chapter 2.2[link] ). Higher-nested list levels are permitted for MIF data (Allen et al., 1995[link]; see Chapter 2.4[link] for a description of the MIF format). Fig. 2.5.6.1[link] shows MIF data specifying a 2D chemical molecular diagram. The first four items in the category DISPLAY are in a level 1 list and the next two items in the category DISPLAY_CONN are in a level 2 list. Note that, according to the STAR File syntax, the nest level is automatically incremented after the first four values, and only decremented when a stop_ signal is encountered.

[Figure 2.5.6.1]

Figure 2.5.6.1 | top | pdf |

(a) Hypothetical example and (b) the typical definition of nested items.

Additional _list attributes for specifying relational dependencies between data items are described in the next attribute group.

Type attributes are used to specify the form of data. The attribute _type is restricted to the states numb, char and null that code for a number, a text string and a dictionary descriptor, respectively. The implications of this typing, in terms of how numbers or character strings are interpreted, is not specified by the CIF syntax. That is, a `number' is simply a string of characters having one of several possible representations (e.g. as an integer, a floating point or in scientific notation) and it is up to the parsing software to interpret these strings appropriately. The same applies in the treatment of text strings defined as `character'. Such strings may be bounded by white space, quotation characters or, in the case of multi-line text, by semicolon characters in column 1 of a line.

The attribute _type_conditions is used to identify application-specific conditions that apply to the typing of data items. This attribute is used to alert parsing software of string constructions that may disrupt the normal identification and validation of data types. The permitted attribute states are none, esd (and its preferred synonym su) and seq. In the definition example in Fig. 2.5.5.3[link] the code esd signals that cell-length values are measurements and may have a standard uncertainty value appended in parentheses. Fig 2.5.5.8 indicates the use of the code su for the same purpose. A full description of _type_conditions states is given in the DDL1 dictionary in Chapter 4.9[link] .

If a data item consists of a concatenation of values, the attribute _type_construct may be used to specify the encoding algorithm for the component values. The language used for this algorithm is POSIX regex (IEEE, 1991[link]). The specification of _type_construct can include the data names of other defined items. Validation software interprets this attribute as format specifications and constraints, and expands the embedded data items according to their separate definition. For example, the chronological date is a composite of day, month and year. These may be represented in many different ways and the _type_construct attribute enables a specific date representation to be defined. The two definitions shown in Fig. 2.5.6.2[link] illustrate how a date value of the construction `1995/03/25' may be embedded into the dictionary definitions (the month and day definitions have been omitted here for brevity).

[Figure 2.5.6.2]

Figure 2.5.6.2 | top | pdf |

Definition example: type constructions.

Units attributes specify the measurement units permitted for a numerical data item. The attribute _units specifies a code that uniquely identifies the measurement units. A description of the units identified by the code is given by the attribute _units_detail. Typical uses of this attribute are shown in Fig. 2.5.5.8[link].

2.5.6.4. Relational attributes

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This class of attributes is used to describe special relationships and dependencies between data items. These attributes are machine parsable and are formally defined in the DDL1 dictionary in Chapter 4.9[link] . They are [Scheme scheme5]

The attribute _category is used to specify to which group, or basis set, a data item belongs. The value of this attribute is a name string that identifies the group and it is usually the leading part of the tags for all items in this group. Data items in a list must have the same category value. Data items in the same category may, however, be divided into different lists, provided each list contains an appropriate key data item (see _list_reference below).

List-link attributes are used to specify dependencies between data items in different lists. The attribute _list_link_parent identifies an item in another list from which the defined item was derived. The parent data item, or items in the case of irreducible sets, must have a unique value within its own list. The _list_link_child attribute is declared in the definition of a parent item and identifies items in other lists that depend implicitly on the defined data item being present in the same data instantiation. The functionalities of these two attributes mirror each other. The parent item must be present in any data instantiation containing the child items, but not the converse. The definition examples in Figs 2.5.5.6[link] and 2.5.5.7[link] illustrate the use of these attributes.

The attributes _list_mandatory and _list_reference are also connected to each other. The former signals (with values of yes or no) whether the presence of a data item is essential to preserving the validity of a list of items. The latter attribute identifies the data item in the list that provides the unique key value to each packet or row of items in a list. A packet is made up of listed values, one for each item in the name list (i.e. the packet size matches the number of data names at the head of the list). The _list_reference attribute identifies items that are the keys to specific packets in the list. In Example 2 of Fig. 2.5.5.5[link] the key item is _atom_site_label and the listed labels S1, S2, N1 and C1 must be unique.

The attribute _list_uniqueness is used to identify items that must be unique for a list to be valid and accessible. This attribute is similar to _list_reference except that it appears only in a definition in which _list_mandatory is set to yes. This simplifies validation because it may be used as the placeholder for all items that jointly identify the uniqueness of a list packet. This is in contrast to the attribute _list_reference, which appears in the definition of every item dependent on this item.

Relational attributes are used to link equivalent data. The _related_item attribute identifies items related to the defined data item. The nature of this relationship is specified with the _related_function attribute according to the restricted value states of alternate, convention, conversion and replace. The definition of these states is detailed in Chapter 4.9[link] . Relational attributes are used to provide equivalent data items, to replace definitions when definitions are superseded or to change access pathways. These facilities are for archives, because they enable old data to be accessed and the associated definitions to remain in a dictionary even when superseded by new definitions. The old and new definitions are linked by these attributes so that all related data items can be validated and accessed.

2.5.6.5. Dictionary registration attributes

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This class of attributes is used to register the dictionary version and audit information. They are [Scheme scheme6]

Dictionary attributes are used to record the creation and update history of a dictionary. The attribute _dictionary_history specifies the entry and update information of the dictionary, and _dictionary_name specifies the generic name of the electronic file containing the dictionary (the actual name of the file can vary from site to site). The attributes _dictionary_version and _dictionary_update specify the version number and the date of the last change in the dictionary. Both items represent important external reference information. An example application of these attributes is shown in Fig. 2.5.5.2[link].

References

IEEE (1991). IEEE Standard for Information Technology – Portable Operating System Interface (POSIX) – Part 2: Shell and utilities, Vol. 1, IEEE Standard 1003.2–1992. New York: The Institute of Electrical and Electronic Engineers, Inc.
Allen, F. H., Barnard, J. M., Cook, A. F. P. & Hall, S. R. (1995). The Molecular Information File (MIF): core specifications of a new standard format for chemical data. J. Chem. Inf. Comput. Sci. 35, 412–427.








































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