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Re: [dddwg] DDDWG update for the BCA


Very nice abstract
Wladek
On 1/15/2016 12:09 PM, Brian McMahon wrote:> Dear Colleagues>> John and I are proposing to submit the attached abstract for> the forthcoming British Crystallographic Association Spring> Meeting in Nottingham.>> Comments welcomed.>> Best regards> Brian> _________________________________________________________________________> Brian McMahon                                       tel: +44 1244 342878> Research and Development Officer                    fax: +44 1244 314888> International Union of Crystallography            e-mail:  bm@iucr.org> 5 Abbey Square, Chester CH1 2HU, England>> Access to raw diffraction data; current practice in article linking> to 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 global> membership of crystallographers, has been working now for over 4 years> to examine the issues and prospects for linking to raw diffraction> data sets from publications. Considerable headway has been made in the> last year, which we will summarise with examples. Recently, a number> of problems with structures of proteins, their ligands, nucleic acids,> carbohydrates, bound metals, etc. have been identified and discussed> in several publications (see for example [1]). There are now in> addition new initiatives to create pilot resources for archiving the> original experimental 'raw' data. This is because raw diffraction> images may be useful for improving individual Protein Data Bank 'bad> apple' deposits, for instructional purposes, and as training sets for> methods developers. There are also challenges posed by recalcitrant,> difficult structures for which 'crowd-efforts' to solve them might be> appropriate. Extensive detailed discussion of the benefits of access> to raw diffraction data can be found in a set of articles in the> October 2014 issue of Acta Crystallographica D. To manage storage of,> and access to, such data sets, we recommend a policy of generating a> permanent digital object identifier (DOI) for data sets worth> retaining; increasingly, tools are in place for organisations that> archive data to register a DOI for each of their raw data> sets. Examples of recent relevant data archiving efforts are the NIH> Big Data to Knowledge (BD2K) initiative, led by Wladek Minor at the> University of Virginia, and a number of other resources, such as> http://www.proteindiffraction.org/ (USA), http://zenodo.org (Europe),> https://store.synchrotron.org.au/public_data/, and Structural Biology> Data Grid https://data.sbgrid.org/ (USA). The BD2K initiative is by> far the largest of these and currently comprises almost 2900 indexable> and searchable diffraction experiments. For published articles a major> development is that the IUCr Journals have recently started linking> their publications with primary data sets in institutional> repositories; this includes articles in the journals IUCrJ,> J. Appl. Cryst., Acta Crystallographica D and F.  As an example, JRH> and co-workers have made available via the University of Manchester> eScholar Repository all the raw data diffraction images of a suite of> crystal structure studies on the binding of cancer compounds (platins)> to histidine in a protein. See, for instance, Tanley et al. (2012) and> the associated raw data (doi:10.15127/1.215887, resolving to> https://www.escholar.manchester.ac.uk/uk-ac-man-scw:215887). In all,> some twenty individual raw diffraction data sets are available. This> means that for this group of crystal structure analyses there is Gold> Open Access to the publications, the PDB files and the raw data.>> Acknowledgements>> We are grateful for numerous interactions these last four years with> the University of Manchester 'JRULM' Library staff with> responsibilities for data deposition in their eScholar publications> and 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 list> dddwg@iucr.org> http://mailman.iucr.org/cgi-bin/mailman/listinfo/dddwg

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