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Title: The living publication

Within the ICSTI Insights Series we offer three articles on the 'living publication' that is already available to practitioners in the important field of crystal structure determination and analysis. While the specific examples are drawn from this particular field, we invite readers to draw parallels in their own fields of interest. The first article describes the present state of the crystallographic living publication, already recognized by an ALPSP (Association of Learned and Professional Society Publishers) Award for Publishing Innovation in 2006. The second article describes the potential impact on the record of science as greater post-publication analysis becomes more common within currently accepted data deposition practices, using processed diffraction data as the starting point. The third article outlines a vision for the further improvement of crystallographic structure reports within potentially achievable enhanced data deposition practices, based upon raw (unprocessed) diffraction data. The IUCr in its Commissions and Journals has for many years emphasized the importance of publications being accompanied by data and the interpretation of the data in terms of atomic models. This has been followed as policy by numerous other journals in the field and its cognate disciplines. This practice has been well served by databases and archiving institutionsmore » such as the Protein Data Bank (PDB), the Cambridge Crystallographic Data Centre (CCDC), and the Inorganic Crystal Structure Database (ICSD). Normally the models that are archived are interpretations of the data, consisting of atomic coordinates with their displacement parameters, along with processed diffraction data from X-ray, neutron or electron diffraction studies. In our current online age, a reader can not only consult the printed word, but can display and explore the results with molecular graphics software of exceptional quality. Furthermore, the routine availability of processed diffraction data allows readers to perform direct calculations of the electron density (using X-rays and electrons as probes) or the nuclear density (using neutrons as probe) on which the molecular models are directly based. This current community practice is described in our first article. There are various ways that these data and tools can be used to further analyze the molecules that have been crystallized. Notably, once a set of results is announced via the publication, the research community can start to interact directly with the data and models. This gives the community the opportunity not only to read about the structure, but to examine it in detail, and even generate subsequent improved models. These improved models could, in principle, be archived along with the original interpretation of the data and can represent a continuously improving set of interpretations of a set of diffraction data. The models could improve both by correction of errors in the original interpretation and by the use of new representations of molecules in crystal structures that more accurately represent the contents of a crystal. These possible developments are described in our second article. A current, significant, thrust for the IUCr is whether it would be advantageous for the crystallographic community to require, rather than only encourage, the archiving of the raw (unprocessed) diffraction data images measured from a crystal, a fibre or a solution. This issue is being evaluated in detail by an IUCr Working Group (see http://forums.iucr.org). Such archived raw data would be linked to and from any associated publications. The archiving of raw diffraction data could allow as yet undeveloped processing methods to have access to the originally measured data. The debate within the community about this much larger proposed archiving effort revolves around the issue of 'cost versus benefit'. Costs can be minimized by preserving the raw data in local repositories, either at centralized synchrotron and neutron research institutes, or at research universities. Archiving raw data is also perceived as being more effective than just archiving processed data in countering scientific fraud, which exists in our field, albeit at a tiny level of occurrences. In parallel developments, sensitivities to avoiding research malpractice are encouraging Universities to establish their own data repositories for research and academic staff. These various 'raw data archives', would complement the existing processed data archives. These archives could however have gaps in their coverage arising from a lack of resources. Nevertheless we believe that a sufficiently large raw data archive, with reasonable global coverage, could be encouraged and have major benefits. These possible developments, costs and benefits, are described in our third and final article on 'The living publication'.« less
Authors:
 [1]
  1. Los Alamos National Laboratory
Publication Date:
OSTI Identifier:
1043003
Report Number(s):
LA-UR-12-21868
TRN: US1203073
DOE Contract Number:
AC52-06NA25396
Resource Type:
Technical Report
Research Org:
Los Alamos National Laboratory (LANL)
Sponsoring Org:
DOE/LANL
Country of Publication:
United States
Language:
English
Subject:
74 ATOMIC AND MOLECULAR PHYSICS; 99 GENERAL AND MISCELLANEOUS//MATHEMATICS, COMPUTING, AND INFORMATION SCIENCE; ATOMIC MODELS; CRYSTAL STRUCTURE; CRYSTALLOGRAPHY; DATA; DATA BASE MANAGEMENT; ELECTRON DENSITY; ELECTRON DIFFRACTION; INFORMATION RETRIEVAL; INFORMATION SYSTEMS; MOLECULAR MODELS; NUCLEAR MATTER