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The acronym CIF is used both for the Crystallographic Information File, the data exchange standard file format of Hall, Allen & Brown (1991), and for the Crystallographic Information Framework, a broader system of exchange protocols based on data dictionaries and relational rules expressible in different machine-readable manifestations, including, but not restricted to, Crystallographic Information File and XML.
CIF was developed by the IUCr Working Party on Crystallographic Information in an effort sponsored by the IUCr Commission on Crystallographic Data and the IUCr Commission on Journals. CIF was adopted in 1990 as a standard file structure for the archiving and distribution of crystallographic information. It is now well established and is in regular use for reporting crystal structure determinations to Acta Crystallographica and other journals. It is often cited as a model example of integrating data and textual information for data-centric scientific communication.
As a granular, structured format, CIF was well suited to the telegraphic style of structure reports required by Acta Crystallographica Section C: Crystal Structure Communications, and was immediately adopted by IUCr journals as a submission medium for this journal. It soon became the mandatory submission format to Acta C, and the mandatory format for supplementary structural data, and subsequently for structure factors, for all IUCr journals.
Automated procedures could then be developed for checking the submitted structural data. This allowed routine technical assessment of all submitted structures (although manual validation was already carried out by many conscientious Co-editors), and the number of erroneous space-group determinations and other technical errors in structure determinations declined significantly. The validation procedures were subsequently developed into the web-based checkCIF service, supported and used by other publishers and available as a general resource to the community for independent validation and assessment of the technical quality of a structure determination.
Extensions of CIF were rapidly developed to describe powder diffraction, modulated structures and electron density studies. Other extensions have followed over the years, including, recently, a description of crystallographic restraints and constraints, and, currently under review, an extension for crystallographic twinning.
An ambitious project to extend CIF to the complete description of protein structure experiments and models resulted in major enhancements to the underlying data model. The resulting mmCIF format formed the basis for the PDB database of protein structures as refactored by the Research Collaboratory for Structural Biology (RCSB) in 1999. Deposit of structure factors to the PDB became possible with the adoption of an mmCIF-based format for experimental data. The PDBx exchange format continues to build on the original mmCIF dictionary and interfaces with extensions for non-crystallographic methods and procedures in protein structure determination and characterisation (Westbrook et al., 2005). An XML format based on the same underlying data model is routinely used to maintain synchronicity between the international partners of the Worldwide Protein Data Bank.
Another important development, beginning in the late 1990s, has been the specification of imgCIF and its corresponding binary format CBF (the 'Crystallographic Binary File') for capturing and exchanging image data (Bernstein & Hammersley, 2005). This provides a common format across the diversity of detector manufacturers, and is currently under close consideration for its possible role in promoting strategies for the routine deposition of primary diffraction image data.
In 2006 the importance of CIF and the value of checkCIF were recognised by the Award for Publishing Innovation of the Association of Learned and Professional Society Publishers (ALPSP). In their report, the judges 'were impressed with the way in which CIF and checkCIF are easily accessible and have served to make critical crystallographic data more consistently reliable and accessible at all stages of the information chain, from authors, reviewers and editors through to readers and researchers. In doing so, the system takes away the donkeywork from ensuring that the results of scientific research are trustworthy without detracting from the value of human judgement in the research and publication process'.
Research has been under way in recent years to develop a new formalism within the CIF framework for specifying data definitions with greater precision, and with machine-readable methods for expressing relations between distinct data items (Spadaccini & Hall, 2012). This will allow automated generation of derivable data that are absent from a particular file, provided all the relevant parent data are present. This new formalism is not intended in the short term to replace the existing CIF format in routine practice, but it does have the potential to provide a unifying computational framework for applications requiring CIF input from different subject areas.
References
Bernstein, H. J. & Hammersley, A. P. (2005). Specification of the Crystallographic Binary File (CBF/imgCIF), in International Tables for Crystallography, Volume G: Definition and exchange of crystallographic data, S. R. Hall & B. McMahon, Editors. 2005, Springer: Dordrecht, The Netherlands. pp. 37-43.
Hall, S. R., Allen, F. H. & Brown, I. D. (1991). The Crystallographic Information File (CIF): a New Standard Archive File for Crystallography. Acta Cryst. A47, 655-685.
Spadaccini, N. & Hall, S. R. (2012). DDLm: a new dictionary definition language. J. Chem. Inf. Model. 52, 1907--1916.
Westbrook, J., Yang,, H., Feng, Z. & Berman, H. M. (2005). The use of mmCIF architecture for PDB data management, in International Tables for Crystallography, Volume G: Definition and exchange of crystallographic data, S. R. Hall & B. McMahon, Editors. 2005, Springer: Dordrecht, The Netherlands. pp. 539-543.