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[dddwg] DDDWG update for the BCA

  • To: dddwg@iucr.org
  • Subject: [dddwg] DDDWG update for the BCA
  • From: Brian McMahon <bm@iucr.org>
  • Date: Fri, 15 Jan 2016 17:09:05 +0000
Dear Colleagues
John and I are proposing to submit the attached abstract forthe forthcoming British Crystallographic Association SpringMeeting in Nottingham.
Comments welcomed.
Best regardsBrian_________________________________________________________________________Brian McMahon                                       tel: +44 1244 342878Research and Development Officer                    fax: +44 1244 314888International Union of Crystallography            e-mail:  bm@iucr.org5 Abbey Square, Chester CH1 2HU, England
Access to raw diffraction data; current practice in article linkingto raw diffraction data 
John R Helliwell[a]* and Brian McMahon[b][a]	School of Chemistry, University of Manchester, M13 9PL, UK[b]	IUCr, 5 Abbey Square, Chester CH1 2HU, UK
john.helliwell@manchester.ac.uk 
The IUCr Diffraction Data Deposition Working Group, with a globalmembership of crystallographers, has been working now for over 4 yearsto examine the issues and prospects for linking to raw diffractiondata sets from publications. Considerable headway has been made in thelast year, which we will summarise with examples. Recently, a numberof problems with structures of proteins, their ligands, nucleic acids,carbohydrates, bound metals, etc. have been identified and discussedin several publications (see for example [1]). There are now inaddition new initiatives to create pilot resources for archiving theoriginal experimental 'raw' data. This is because raw diffractionimages may be useful for improving individual Protein Data Bank 'badapple' deposits, for instructional purposes, and as training sets formethods developers. There are also challenges posed by recalcitrant,difficult structures for which 'crowd-efforts' to solve them might beappropriate. Extensive detailed discussion of the benefits of accessto raw diffraction data can be found in a set of articles in theOctober 2014 issue of Acta Crystallographica D. To manage storage of,and access to, such data sets, we recommend a policy of generating apermanent digital object identifier (DOI) for data sets worthretaining; increasingly, tools are in place for organisations thatarchive data to register a DOI for each of their raw datasets. Examples of recent relevant data archiving efforts are the NIHBig Data to Knowledge (BD2K) initiative, led by Wladek Minor at theUniversity of Virginia, and a number of other resources, such ashttp://www.proteindiffraction.org/ (USA), http://zenodo.org (Europe),https://store.synchrotron.org.au/public_data/, and Structural BiologyData Grid https://data.sbgrid.org/ (USA). The BD2K initiative is byfar the largest of these and currently comprises almost 2900 indexableand searchable diffraction experiments. For published articles a majordevelopment is that the IUCr Journals have recently started linkingtheir publications with primary data sets in institutionalrepositories; this includes articles in the journals IUCrJ,J. Appl. Cryst., Acta Crystallographica D and F.  As an example, JRHand co-workers have made available via the University of ManchestereScholar Repository all the raw data diffraction images of a suite ofcrystal structure studies on the binding of cancer compounds (platins)to histidine in a protein. See, for instance, Tanley et al. (2012) andthe associated raw data (doi:10.15127/1.215887, resolving tohttps://www.escholar.manchester.ac.uk/uk-ac-man-scw:215887). In all,some twenty individual raw diffraction data sets are available. Thismeans that for this group of crystal structure analyses there is GoldOpen Access to the publications, the PDB files and the raw data. 
Acknowledgements
We are grateful for numerous interactions these last four years withthe University of Manchester 'JRULM' Library staff withresponsibilities for data deposition in their eScholar publicationsand data repository, notably Chris Gibson and Berrisford Edwards. 

[1] Wladek Minor, Zbigniew Dauter, John R. Helliwell, Mariusz Jaskolski and Alexander Wlodawer (2016) 'Safeguarding structural data repositories against bad apple.' Structure. In the press._______________________________________________dddwg mailing listdddwg@iucr.orghttp://mailman.iucr.org/cgi-bin/mailman/listinfo/dddwg

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