Published August 18, 2019 | Version v1
Presentation Open

Overview of the new opportunities in and a harmonisation of peer review of "data with validation report with article narrative" practices

Authors/Creators

  • 1. University of Manchester

Description

Observing the work of an Acta Cryst. C Co-editor directly for several years (my wife and colleague Dr Madeleine Helliwell) inspired me to look to improve the IUCr biological journals to follow the Acta Cryst. C standard. My effort as Editor-in-Chief at the IUCr Congress in Geneva in 2002 was not approved at the Open Commission of Biological Macromolecules meeting. Later I realised, in my refereeing, that I should insist on having from the authors, via the editor, the to-be-released PDB coordinates and structure factors as well as the PDB Validation Report and article. [1] If I did not receive these then I would not undertake the refereeing task, of course promptly informing the editor. My whole refereeing experience was transformed, being much more thorough and satisfying. Basically I find that the Validation Report is invaluable in checking the general aspects of a PDB deposition and my refereeing of the data, with my own calculations, addresses the specific aspects of a study. Meanwhile a new theme involves the raw data owing to amazing hardware advances. So Gigabyte-, even Terabyte-, sized raw data sets can be preserved. A reader of a publication can revisit the earliest calculation decisions of the authors. My reaction to this new refereeing opportunity over the last two years has been to recommend that authors improve their raw data processing, rather than my moving their diffraction images onto my computer and reprocessing them [1]. Overall, IUCr Journals policy on raw diffraction data is being informed by the IUCr Commissions’ reactions to the IUCr Diffraction Data Deposition Working Group’s Final Report [2]. The first such formal change to Notes for Authors is for biological crystallography [3].

  1. Helliwell, J. R. (2018). Data science skills for referees: biological X-ray crystallography. Crystallogr. Rev. 24, 263-272.
  2. https://www.iucr.org/resources/data/dddwg/final-report (2017). Authored by the Members of the DDDWG.
  3. Helliwell, J. R., Minor, W., Weiss, M. S., Garman, E. F., Read, R. J., Newman, J., van Raaij, M. J., Hajdu, J. & Baker, E. N. (2019). Findable Accessible Interoperable Re-usable (FAIR) diffraction data are coming to protein crystallography. IUCrJ 6, 341–343.

Notes

There is a trend towards ensuring that modern science research data are findable, accessible, interoperable and reusable (FAIR). However, this is something that crystallographers have been achieving for many decades, during which excellent crystallographic databases have always exploited the best available hardware for digital archiving. FAIR is necessary but not sufficient, as physicists would say, as the archived data should also be true facts. So FACT and FAIR are needed for reproducibility. The crystallographic community has developed automatic checking software by pooling its experiences from hundreds of thousands of crystal structure analyses into validation procedures with numerous data file checks on both coordinates and processed diffraction data sets. Alarm alerts can then be scrutinised by journal editors and referees. With such exemplary procedures is there anything to be improved? Crystallographers conclude that there is. Firstly the IUCr journal Acta Cryst. C: Structural Chemistry has always required submission of article with validation report with underpinning data files. Thus the specialist subject expertise of referees can involve their own direct calculations to supplement the automatic checks before article and data set acceptance as versions of record by the editor. This has inspired others to look to improve their own crystallographic disciplines and journals to follow the Acta Cryst. C standard. Secondly the digital archives have enhanced their capacity in recent years owing to amazing hardware advances so that even the Gigabyte-sized raw data sets can also be preserved as versions of record. A reader of a publication can thereby revisit even the earliest calculation decisions of the authors of a publication. As the Royal Society of London puts it: science is about not taking someone's word and so, instead, the science is always in the data. FACT and FAIR, indeed scientific objectivity itself, is possible. This Workshop will address the state of the art in the field and the data science skills hoped for, indeed to be expected, of all those involved in publishing crystallography results, and of results from all the cognate methods such as scattering, microscopy and spectroscopy.

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