PDBx/mmCIF
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mmCIF Early History

'CIF' is an acronym for the Crystallographic Information File. CIF is a subset of STAR (Self-defining Text Archive and Retrieval format [1]). The CIF format is suitable for archiving, in any order, all types of text and numerical data. The goals of CIF are to explore its generality, upward compatibility, flexibility, and to incorporate these in electronic publication.

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. The result of this effort was a dictionary of data items sufficient for archiving the small molecule crystallographic experiment and its results [2]. This dictionary was adopted by the IUCr at its 1990 Congress in Bordeaux. CIF is now the format in which structure papers are submitted to Acta Crystallographica C; software has been developed to automatically typeset a paper from a CIF.

In 1990, the IUCr formed a working group that would expand this dictionary by including data items relevant to the macromolecular crystallographic experiment. This working group was chaired by Paula Fitzgerald and included Enrique Abola, Helen Berman, Phil Bourne, Eleanor Dodson, Art Olson, Wolfgang Steigemann, Lynn Ten Eyck, and Keith Watenpaugh (Upjohn).

The original short term goal of the working group was to fulfill the mandate set by the IUCr: to define mmCIF data names that needed to be included in the CIF dictionary in order to adequately describe the macromolecular crystallographic experiment and its results. Long term goals were also determined: to provide sufficient data names so that the experimental section of a structure paper could be written automatically and to facilitate the development of tools so that computer programs could easily interface with the CIF.

In order to describe the progress of this project and to solicit community feedback, several informal and formal meetings were held. The first meeting, hosted by Eleanor Dodson, convened in April 1993 at the University of York. The attendees included the mmCIF working group, structural biologists and computer scientists. A major focus of the discussion was whether the formal structure of the dictionary that was implemented using the then-current Dictionary Definition Language (DDL 1.0) was adequate to deal with the complexity of the macromolecular data items. Criticisms included the idea that the data typing was not strong enough and that there were no formal links among the data items. A working group was formed to try to address these issues. The second Workshop was hosted by Phil Bourne in Tarrytown, NY in October 1993. The topics at that meeting focused on the development of software tools and the requirements of an enhanced DDL. In October 1994, a workshop hosted by Shoshana Wodak at the Free University of Brussels, resulted in the development of a new DDL that addressed the various problems that had been identified at the previous workshops. The dictionary was cast in this new DDL 2 and was presented at the ACA meeting in Montreal in July 1995.

This dictionary was open for further community review. The dictionary was placed on a World Wide Web site and community comments were solicited via a list server. Lively discussions via this mmCIF list server ensued, resulting in the continuous correction and updating of the dictionary. Software was developed and was also presented on an early mmCIF Resource web site. The tools that were available at this point in time included: CIFtbx2 (Extended CIF Tool Box; Fortran), OOSTAR (applications to manipulate STAR files; Objective-C), pdb2cif (awk script to convert PDB to mmCIF), and CIFLIB (C Language Application Program Interface).

In January 1997, the mmCIF dictionary was completed and submitted to COMCIFS for review, and version 1.0 was released in June 1997[3,4]. A workshop held at Rutgers University in October 1997 was hosted by Helen Berman. Tutorials were presented to demonstrate the use of the various tools that had been developed. Discussion about how to proceed with the maintenance and evolution of the dictionary led to a plan for extending the dictionary using template definitions. Versions of the mmCIF dictionary that followed included new definitions that were reviewed according to this plan.

Acknowledgments

The development of the mmCIF dictionary and the associated DDL 2.2.1 was an enormous task, and any list of contributors to the effort will certainly be incomplete. Many people that have taken the time to think carefully and constructively about all of this. To begin it is important to recognize Syd Hall, David Brown and Frank Allen, who began the entire CIF effort and who recruited us to do the extensions for macromolecular structure.

The above history lists the people who were members of the original working party, but the number of people who contributed to the original design of the mmCIF data structure is in fact much larger and includes contributions from Steve Bryant, Vivian Stojanoff, Jean Richelle, Eldon Ulrich, and Brian Toby.

There are also the people who realized the shortcomings of the original DDL, and worked hard to convince us that a more rigorous underpinning for the dictionary would been needed. Among them are Michael Scharf, Peter Gray, Peter Murray-Rust, Dave Stampf, and Jan Zelinka.

Writing the dictionary and developing the new DDL were just the starting points for evaluation and critique, and this effort has been greatly aided by the input from COMCIFS, the IUCr committee with oversight over this process (Brian McMahon, Coordinating Secretary). But the real process of review, after the dictionary was released to the public for comment in August of 1995, has involved a much larger cast. This review received valuable input from Frances Bernstein, Herbert Bernstein, Dale Tronrud, and Peter Keller.

The dictionary development effort was also enabled by the staff of the Nucleic Acid Database at Rutgers University, who have dealt with many of the technical issues of implementation of mmCIF with real data. So we would also like to thank Anke Gelbin, Shu-Hsin Hsieh, and Christine Zardecki (the author of this Web page.)

Without the three CIF workshops, this effort would never have taken the shape and focus. The organizers of those workshops include: Eleanor Dodson, Phil Bourne, Shoshana Wodak and Helen Berman, and with the funding provided by ESF, EU, NSF, and DOE.

[1] S.R. Hall (1991) The STAR File: A new format for electronic data transfer and archiving. J. Chem. Inf. Comp. Sci., 31, 326-333.

[2] S.R. Hall, F.H. Allen and I.D. Brown (1991) A new standard archive file for crystallography. Acta Cryst., A47, 655-685.

[3] P.M.D. Fitzgerald, H.M. Berman, P.E. Bourne, B. McMahon, K. Watenpaugh, and J. Westbrook (1996) The mmCIF dictionary: community review and final approval. IUCr Congress and General Assembly, August 8-17, Acta Cryst., A52 Supplement. Seattle, WA. MSWK.CF.06.

[4] P. Bourne, H.M. Berman, K. Watenpaugh, J. Westbrook, and P.M.D. Fitzgerald (1997) The macromolecular Crystallographic Information File (mmCIF). Meth. Enzymol., 277, 571-590.