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. 3.6, pp. 194-195

Section 3.6.9. File metadata

P. M. D. Fitzgerald,a* J. D. Westbrook,b P. E. Bourne,c B. McMahon,d K. D. Watenpaughe and H. M. Bermanf

aMerck Research Laboratories, Rahway, New Jersey, USA,bProtein Data Bank, Research Collaboratory for Structural Bioinformatics, Rutgers, The State University of New Jersey, Department of Chemistry and Chemical Biology, 610 Taylor Road, Piscataway, New Jersey, USA,cResearch Collaboratory for Structural Bioinformatics, San Diego Supercomputer Center, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0537, USA,dInternational Union of Crystallography, 5 Abbey Square, Chester CH1 2HU, England,eretired; formerly Structural, Analytical and Medicinal Chemistry, Pharmacia Corporation, Kalamazoo, Michigan, USA, and fProtein Data Bank, Research Collaboratory for Structural Bioinformatics, Rutgers, The State University of New Jersey, Department of Chemistry and Chemical Biology, 610 Taylor Road, Piscataway, New Jersey, USA
Correspondence e-mail:  paula_fitzgerald@merck.com

3.6.9. File metadata

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As in the core CIF dictionary, information about the source and the revision history of an mmCIF may be given in the AUDIT group of categories: AUDIT, AUDIT_AUTHOR, AUDIT_CONTACT_AUTHOR and AUDIT_CONFORM (Section 3.6.9.1[link]). However, the mmCIF dictionary differs from the core CIF dictionary in the way it expresses relationships between data blocks: instead of the core AUDIT_LINK category, mmCIF has two categories, ENTRY and ENTRY_LINK, that essentially fulfil the same role but are classified in a distinct category group (Section 3.6.9.2[link]).

3.6.9.1. History of a data block

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The categories describing the history of a data block are as follows:

AUDIT group
 AUDIT
 AUDIT_AUTHOR
 AUDIT_CONFORM
 AUDIT_CONTACT_AUTHOR

Data items in these categories are as follows:

(a) AUDIT [Scheme scheme209]

(b) AUDIT_AUTHOR [Scheme scheme210]

(c) AUDIT_CONFORM [Scheme scheme211]

(d) AUDIT_CONTACT_AUTHOR [Scheme scheme212]

The bullet ([\bullet]) indicates a category key. Where multiple items within a category are marked with a bullet, they must be taken together to form a compound key. Items in italics have aliases in the core CIF dictionary formed by changing the full stop (.) to an underscore (_).

The data items in these categories are used in the same way in the mmCIF dictionary as in the core CIF dictionary (see Section 3.2.6[link] ). The data item _audit.revision_id has been added to the AUDIT category to provide the formal category key required by the DDL2 data model. The core data item _audit_block_code has been replaced by _entry.id (see Section 3.6.9.2[link]).

3.6.9.2. Links between data blocks

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The categories describing links between data blocks are as follows:

ENTRY group
 ENTRY
 ENTRY_LINK
AUDIT group
 AUDIT_LINK

Data items in these categories are as follows:

(a) ENTRY [Scheme scheme213]

(b) ENTRY_LINK [Scheme scheme214]

(c) AUDIT_LINK [Scheme scheme215]

The bullet ([\bullet]) indicates a category key. Where multiple items within a category are marked with a bullet, they must be taken together to form a compound key. The arrow ([\rightarrow]) is a reference to a parent data item. Items in italics have aliases in the core CIF dictionary formed by changing the full stop (.) to an underscore (_).

The sole data item in the category ENTRY, _entry.id, is a label that identifies the current data block. This label is used as the formal key in several categories that record information that is relevant to the entire data block (e.g. _cell.entry_id, _geom.entry_id), so care should be taken to select a label that is informative and unique.

Data items in the ENTRY_LINK category record the relationships between the current data block and other data blocks within the current file which may be referenced in the current data block. Since there are no formal constraints on the value of _entry.id assigned to each data block, authors must take care to ensure that an mmCIF comprised of several distinct data blocks uses a different value for _entry.id in each block.

As mentioned in the introductory paragraph of Section 3.6.9[link] , the ENTRY_LINK category is used in mmCIF applications instead of the core category AUDIT_LINK. The latter is retained formally in the mmCIF dictionary for strict compatibility with the core dictionary, and the data items in this category, _audit_link.blockcode and _audit_link.block_description, are aliased to corresponding core data names (see Section 3.2.6.1[link] ). Their use is not recommended in mmCIF applications.

3.6.9.3. Other category classifications

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The following categories, already described elsewhere in this chapter, are included in other formal category groups:

Compliance with earlier dictionaries
COMPLIANCE group
 DATABASE
Compatibility with PDB format files
PDB group
 DATABASE_PDB_CAVEAT
 DATABASE_PDB_MATRIX
 DATABASE_PDB_REMARK
 DATABASE_PDB_REV
 DATABASE_PDB_REV_RECORD
 DATABASE_PDB_TVECT

The COMPLIANCE group includes categories that appear in the mmCIF dictionary for the sole purpose of ensuring compliance with earlier dictionaries. They are not intended for use in the creation of new mmCIFs. As was discussed in Section 3.6.8.3[link], the DATABASE category of the core CIF is replaced in mmCIF by the more structured DATABASE_2 category. Thus the core CIF DATABASE category appears in the mmCIF COMPLIANCE group. At the time of writing (2005), DATABASE is the only category in the COMPLIANCE group.

The PDB group includes a number of categories that record unstructured information imported from various records in Protein Data Bank (PDB) format files. These categories are also part of the DATABASE group and were discussed in Section 3.6.8.3.2[link].[link]








































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