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International
Tables for Crystallography Volume G Definition and exchange of crystallographic data Edited by S. R. Hall and B. McMahon © International Union of Crystallography 2006 |
International Tables for Crystallography (2006). Vol. G. ch. 3.6, p. 192
Section 3.6.8.3.1. Related database entries
P. M. D. Fitzgerald,a* J. D. Westbrook,b P. E. Bourne,c B. McMahon,d K. D. Watenpaughe and H. M. Bermanf
a
Merck 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 |
Data items in these categories are as follows:
![[Scheme scheme191]](/schemes/Gach3o6scheme191.gif)
![[Scheme scheme192]](/schemes/Gach3o6scheme192.gif)
The bullet (![[\bullet]](/teximages/a1ach2o1/a1ach2o1fi16.svg)
) 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]](/teximages/abch3o1/abch3o1fi527.svg)
) 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 DATABASE category is retained in the mmCIF dictionary, but only for consistency with the core dictionary.
The role of the data items in the DATABASE_2 category is to store identifiers assigned by one or more databases to the structure described in the mmCIF. In the data model used in the core CIF dictionary, each database has an individual data item. The data model in mmCIF is more general. It comprises the data items _database_2.database_id, which identifies the database, and _database_2.database_code, which is the code assigned by the database to the entry. Thus a new database can be referred to without needing to add an additional data item to the dictionary. If a structure has been deposited in more than one database, the values of _database_2.database_id and _database_2.database_code can be looped.
The institutions and individual databases recognized in the DATABASE_2 category in the current version of the mmCIF dictionary are CAS (Chemical Abstracts Service), CSD (Cambridge Structural Database), ICSD (Inorganic Crystal Structure Database), MDF (Metals Data File), NDB (Nucleic Acid Database), NBS (the Crystal Data database of the National Institute of Standards and Technology, formerly the National Bureau of Standards), PDB (Protein Data Bank), PDF (Powder Diffraction File), RCSB (Research Collaboratory for Structural Bioinformatics) and EBI (European Bioinformatics Institute). It is intended that new databases will be added to this list on an ongoing basis; the purpose of specifying a list of possible databases in the dictionary is to ensure that each database is referenced consistently.
