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Draft COMCIFS 2016 report

  • To: "Discussion list of the IUCr Committee for the Maintenance of the CIF Standard (COMCIFS)" <comcifs@iucr.org>
  • Subject: Draft COMCIFS 2016 report
  • From: James Hester <jamesrhester@gmail.com>
  • Date: Thu, 23 Mar 2017 12:19:37 +1100
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Please see below a draft report for the preceding year for submission to the IUCr executive.  Please let me know as soon as possible of any errors or omissions.


COMCIFS report 2016

COMCIFS is tasked with maintaining and developing the Crystallographic
Information Framework (CIF) on behalf of the IUCr.

New dictionaries

A dictionary describing magnetic structures (magCIF) was produced
by the Commission on Magnetic Structures with technical advice
from COMCIFS members.  It has been approved by COMCIFS and has
seen rapid adoption in software dealing with magnetic structures.

Updating legacy dictionaries

At the 2014 Montreal meeting, COMCIFS resolved that all dictionaries
written in the legacy DDL1 language would be converted to the new DDLm
language.  A DDLm version of the core CIF dictionary, upon which most
other dictionaries depend, was approved by COMCIFS towards the end of
2016. Draft DDLm versions of the remaining dictionaries are being sent
out to the original authors for checking.  As part of this process,
authors are able to provide any updates and new definitions, and will
be invited to contribute or update chapters for the second edition of
International Tables Volume G.

Macromolecular standards

The wwPDB continued to promote CIF usage in the macromolecular
community, with sponsorship of SASCIF expansion efforts [1] and
hybrid methods dictionary extensions [2].

The new wwPDB OneDep Deposition & Annotation system [3]
(deposit.wwpdb.org) released with added support for NMR and 3DEM
Structures.  The OneDep system is built on a PDBx/mmCIF data
infrastructure representing all of these experimental methods [4].  The
X-ray refinement applications CCP4/REFMAC and Phenix.Refine both
support the production of PDBx/mmCIF data files ready for deposition.
Current dictionaries used by this system are made available on the
PDBx/mmCIF resources site mmcif.wwpdb.org

Interaction with other data management initiatives

For the past five years, we have worked to achieve interoperability
between imgCIF/CBF and NeXus/HDF5 NXmx in describing metadata for
macromolecular crystallography diffraction images.  This effort has
contributed to successful handling of diffraction images from XFEL
detectors and Dectris Eiger detectors in both CBF and HDF5
formats [5][6][7][8].

Starting in 2016 there have now been four High Data -Rate
Macromolecular Crystallography (HDRMX) meetings (see
http://www.medsbio.org/hdrmx/).  At the most recent HDRMX meeting,
(March 2017) it was agreed to begin mapping both the mmcif and corecif
dictionaries into NeXus, so that complete descriptions of the samples
studied can be included with diffraction image metadata in the
earliest stages of crystallographic studies.  This will facilitate
both publication and archiving.


[1] Extension of the sasCIF format and its applications for data processing and deposition
Kachala, M., Westbrook, J., & Svergun, D. (2016). Journal of Applied Crystallography,
49(Pt 1), 302–310.

[2] https://github.com/ihmwg/IHM-dictionary/blob/master/dictionary_documentation/documentation.md

[3] OneDep: Unified wwPDB System for Deposition, Biocuration, and
Validation of Macromolecular Structures in the PDB Archive Jasmine
Y. Young, John D. Westbrook, Zukang Feng, Raul Sala, Ezra Peisach,
Thomas J. Oldfield9, Sanchayita Sen, Aleksandras Gutmanas, David
R. Armstrong, John M. Berrisford, Li Chen, Minyu Chen, Luigi Di
Costanzo, Dimitris Dimitropoulos10, Guanghua Gao, Sutapa Ghosh,
Swanand Gore, Vladimir Guranovic, Pieter M.S. Hendrickx, Brian
P. Hudson, Reiko Igarashi, Yasuyo Ikegawa, Naohiro Kobayashi,
Catherine L. Lawson, Yuhe Liang, Steve Mading, Lora Mak, M. Saqib Mir,
Abhik Mukhopadhyay, Ardan Patwardhan, Irina Persikova, Luana Rinaldi,
Eduardo Sanz-Garcia, Monica R. Sekharan, Chenghua Shao, G. Jawahar
Swaminathan11, Lihua Tan, Eldon L. Ulrich, Glen van Ginkel, Reiko
Yamashita, Huanwang Yang, Marina A. Zhuravleva, Martha Quesada, Gerard
J. Kleywegt, Helen M. Berman, John L. Markley, Haruki Nakamura, Sameer
Velankar, Stephen K. Burley (2017) Structure , Volume 25 , Issue 3 ,
536 - 545

[4] NMR Exchange Format: a unified and open standard for
representation of NMR restraint data Aleksandras Gutmanas, Paul D
Adams, Benjamin Bardiaux, Helen M Berman, David A Case, Rasmus H Fogh,
Peter Güntert, Pieter M S Hendrickx, Torsten Herrmann, Gerard J
Kleywegt, Naohiro Kobayashi, Oliver F Lange, John L Markley, Gaetano T
Montelione, Michael Nilges, Timothy J Ragan, Charles D Schwieters,
Roberto Tejero, Eldon L Ulrich, Sameer Velankar, Wim F Vranken,
Jonathan R Wedell, John Westbrook, David S Wishart & Geerten W
Vuister,(2015) Nature Structural & Molecular Biology 22, 433–434

[5] Brewster, Aaron S., Johan Hattne, James M. Parkhurst, David
G. Waterman, Herbert J. Bernstein, Graeme Winter, and
N. K. Sauter. "XFEL Detectors and ImageCIF." Computational
Crystallography Newsletter 5 (2014): 19-24.

[6] Förster, Andreas, Stefan Brandstetter, Marcus Müller, and Clemens
Schulze-Briese. "EIGER detectors in biological crystallography."

[7] Bernstein, Herbert J., Babak Andi, Kaden Badalian, Lonny
E. Berman, Dileep K. Bhogadi, Shirish Chodankar, Jonathan DiFabio,
Martin R. Fuchs, Jean Jakoncic, Edwin O. Lazo, Sean McSweeney, Lisa
Miller, Stuart Myers, Dieter K. Schneider, Bruno Seiva Martins, Wuxian
Shi, John Skinner, Hugo Slepicka, Alexei Soares, Vivian Stojanoff,
Robert M. Sweet, Ryan Tappero, and Lin Yang. "Computing
infrastructure, software optimization, and real time analysis for high
data-rate MX." In Scientific Data Summit (NYSDS), 2016 New York,
pp. 1-4. IEEE, 2016.

[8] Hester, James. "A Robust, Format-Agnostic Scientific Data Transfer Framework."
Data Science Journal 15 (2016)

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