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. 85-88

Section 3.1.8. Management of multiple dictionaries

B. McMahona*

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

3.1.8. Management of multiple dictionaries

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So far this chapter has discussed the mechanics of writing dictionary definitions and of assembling a collection of definitions in a single global or local dictionary file. In practice, the set of data names in a CIF data file may include names defined in several dictionary files. A mechanism is required to identify and locate the dictionaries relevant to an individual data file. In addition, because dictionaries are suitable for automated validation of the contents of a data file, it is convenient to be able to overlay the attributes listed in a dictionary with an alternative set that permit validation against modified local criteria. This section describes protocols for identifying, locating and overlaying dictionary files and fragments of dictionary files.

3.1.8.1. Identification of dictionaries relevant to a data file

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A CIF data file should declare within each of its data blocks the names, version numbers and, where appropriate, locations of the global and local dictionaries that contain definitions of the data names used in that block. For DDL1 dictionaries, the relevant identifiers are the items _audit_conform_dict_name, _audit_conform_dict_version and _audit_conform_dict_location, defined in the core dictionary. DDL2 dictionaries are identified by the equivalent items _audit_conform.dict_name, *.dict_version and *.dict_location. For convenience, the DDL1 versions will be used in the following discussion.

The values of the items _audit_conform_dict_name and _audit_conform_dict_version are character strings that match the values of the _dictionary_name and _dictionary_version identifiers in the dictionary that defines the relevant data names. Validation against the latest version of a dictionary should always be sufficient, since every effort is made to ensure that a dictionary evolves only by extension, not by revising or removing parts of previous versions of the dictionary. Nevertheless, including _audit_conform_dict_version is encouraged: it can be useful to confirm which version of the dictionary the CIF was initially validated against.

The data item _audit_conform_dict_location may be used to specify a file name or uniform resource locator (URL). However, a file name on a single computer or network will be of use only to an application with the same view of the local file system, and so is not portable. A URL may be a better indicator of the location of a dictionary file on the Internet, but can go out of date as server names, addresses and file-system organization change over time. The preferred method for locating a dictionary file is to make use of a dynamic register, as described in Section 3.1.8.2[link]. Nevertheless, _audit_conform_dict_location remains a valid data item that may be of legitimate use, particularly in managing local applications.

The following example demonstrates a statement of dictionary conformance in a data file describing a powder diffraction experiment with some additional local data items: [Scheme scheme19] It is clear that the location specified for the local dictionary is only meaningful for applications running on the same computer or network, and therefore the ability to validate against this local dictionary is not portable. On the other hand, it may be that the local data names used by the authors of this CIF are not intended to have meaning outside their own laboratory.

3.1.8.2. The dictionary register

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COMCIFS maintains a register of dictionaries known to it, including the identifying name and version strings within those dictionaries. The register also includes the location of each dictionary, expressed at present as a URL designed to allow retrieval by file transfer protocol (ftp) from the IUCr server. Changes in the location of a particular dictionary file can be made by modifying the entry in the register, avoiding the problem of specifying a URL in a data file that would then become outdated if the dictionary was moved. Dictionary applications can consult the register (according to a protocol outlined below) to locate and retrieve the dictionaries needed for validating data files. It is of course essential that the validation software knows how to locate the register. The location is at present given by the URL ftp://ftp.iucr.org/pub/cifdics/cifdic.register .

The problem of changing URLs has therefore not disappeared completely, but is at least confined to the need to maintain one single address.

Table 3.1.8.1[link] is an extract from the current register. The latest version of the register will always be available from the URL given above.

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CIF dictionary register (maintained as a STAR File)

[Scheme scheme23]

The entries for each dictionary include one with the version string set to `.', representing the current version; this is the version that should be retrieved unless a data file specifies otherwise.

Note that the register may also contain locators for local dictionaries constructed by owners of reserved prefixes (Section 3.1.2.2[link]) when the owner has requested that a dictionary of local names be made publicly available. An appropriate name for a local dictionary in the register ( _dictionary_name or _dictionary.title for DDL1 or DDL2 dictionaries, respectively) would be cif_local_myprefix.dic, where the string indicated by myprefix is one of the prefixes reserved for private use by the author of the dictionary (see Section 3.1.2.2[link]). This scheme complements the naming convention for public dictionaries.

3.1.8.3. Locating a dictionary for validation

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The following protocol applies to the creation and use of software designed to locate the dictionaries referenced by a data file and validate the data file against them. The protocol is necessary to address the issues that arise because dictionaries evolve through various audited versions, because not all dictionaries referenced by a data file may be accessible, and because data files might not in practice contain pointers to their associated dictionaries.

Software source code for applications that use CIF dictionaries to validate the contents of data files should be distributed with a copy of the most recent version of the register of dictionaries, and with the URL of the master copy hard-coded. Library utilities should be provided that permit local cacheing of the register file and the ability to download and replace the cached register at regular intervals. Individual dictionary files located and retrieved through the use of the register should also be cached locally, to guard against temporary unavailability of network resources.

Each CIF data file should contain a reference to one or more dictionary files against which the file may be validated. At the very least this will be _audit_conform_dict_name ( _audit_conform.dict_name for DDL2 files) (N). *_version (V) and *_location (L) are optional. In the event that no dictionaries are specified, the default validation dictionary should be that identified as having N = cif_core.dic and V = `.' (i.e. the most recent version of the core dictionary). Since dictionaries are intended always to be extended, it is normally enough just to specify the name (and possibly the location).

This default is appropriate for most well formed CIFs, but if it is important to provide formal validation of old CIFs conforming to the earliest printed specification, which used the now-deprecated units extension convention, the dictionary cif_compat.dic may also be added to the default list (Section 3.1.5.4.3[link]).

There is a difficulty associated with assuming this default for CIFs containing DDL2 data names. At present, the DDL2 version of the core dictionary does not exist as a separate file. Most existing CIFs built on the DDL2 model conform to the macromolecular (mmCIF) dictionary, and so best current working practice is to assume a default validation dictionary for DDL2-style CIFs with N = mmcif_std.dic and V = `.' (i.e. the most recent version of the mmCIF dictionary), since this includes the core data names as a subset. However, to anticipate future developments, it is suggested that applications built to validate DDL2 files first search the register for a default entry with N = cif_core.dic, V = `.' and a value of 2 or higher for the relevant DDL version: [Scheme scheme20]

A software application validating against CIF dictionaries should attempt to locate and validate against the referenced dictionaries in the order cited in the data file, according to the following procedure. The terms `warning' and `error' in this procedure are not necessarily messages to be delivered to a user. They may be handled as condition codes or return values delivered to calling procedures instead.

If N, V and L are all given, try to load the file from the location L, or a locally cached copy of the referenced file. If this fails, raise a warning. Then search the dictionary register for entries matching the given N and V. (An appropriate strategy would be to search a locally cached copy of the register, and to refresh that local copy with the latest version from the network if the search fails.) If a successful match is made, try to retrieve the file from the location given by the matching entry in the register (or a locally cached copy with the same N and V previously fetched from the location specified in the register). If this fails, try to load files identified from the register with the same N but progressively older versions V (version numbering takes the form n.m.l…, where n, m, l, … are integers referring to progressively less significant revision levels). Version `.' (meaning the current version) should be accessed before any other numbered version. If this fails, raise a warning indicating that the specified dictionary could not be located.

If N and V but not L are given, try to load locally cached or master copies of the matching dictionary files from the location specified in the register file, in the order stated above, viz: (i) the version number V specified; (ii) the version with version number indicated as `.'; (iii) progressively older versions. Success in other than the first instance should be accompanied by a warning and an indication of the revision actually loaded.

If only N is given, try to load files identified in the register by (i) the version with version number indicated as `.'; (ii) progressively older versions.

If all efforts to load a referenced dictionary fail, the validation application should raise a warning.

If all efforts to load all referenced dictionaries fail, the validation application should raise an error.

For any dictionary file successfully loaded according to this protocol, the validation application must perform a consistency check by scanning the file for internal identifiers ( _dictionary_name, _dictionary_version or the DDL2 equivalents) and ensuring that they match the values of N and V (where V is not `.'). Failure in matching should raise an error.








































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