Data curation in crystallography publisher perspectives
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JISC Data Cluster Consultation Workshop CCLRC, Didcot, Oxon 10 October 2006. Data Curation in Crystallography: Publisher Perspectives. Crystal Structure reports - data-rich scientific articles.

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Data curation in crystallography publisher perspectives

JISC Data Cluster Consultation Workshop

CCLRC, Didcot, Oxon 10 October 2006

Data Curation in Crystallography: Publisher Perspectives


Crystal structure reports data rich scientific articles

Crystal Structure reports - data-rich scientific articles

  • 3-d positional coordinates

  • Atomic motions

  • Molecular geometry

  • Chemical bonding

  • Crystal packing

  • Chemical behaviour arising from structure

  • Two dedicated IUCr journals: Acta Cryst. C, E

  • Important part of scientific discussion in many other titles: Acta Cryst. B, D, F


Data that inform the discussion

Data that inform the discussion

Raw data

(image plate, diffractometer, film)

Derived data

(six-dimensional structural model)

Primary data

(structure factors)


Spectrum of publications

Spectrum of publications

  • Radical new knowledge of crystal/molecular structures (rare)

  • Radical new methods for solving/refining structures (rare)

  • Major contribution to understanding of chemical properties of one or a class of compounds (Acta Cryst. Section B)

  • Significant new information about a compound or group of related compounds (Acta Cryst. Section C)

  • Full description of a new structure (Acta Cryst. Section E)

  • Routine structure determination (Acta E/eBank/chemistry journal)

  • Partial/incomplete structure determination (chemistry journal/lab notebook)


At the edge of the spectrum

At the edge of the spectrum…

  • Supplementary data in chemistry journals

  • Voluntary deposit with curated databases

  • Institutional repositories (universities)

  • Voluntary open-access subject repositories

  • Crystallography service facilities

  • Industrial and pharmaceutical companies

  • Deposit of structure factors

  • Total loss


Data publication at source

Data publication at source

Initiatives such as eBank are particularly valuable:

  • Some prospect of longevity

  • Use of common protocols/federation

  • Address domain-specific concerns

  • Large enough (as federated entities) to discuss special arrangements for archiving (including with publishers)

  • Comprehensive within user base (does not rely on voluntary action)

  • Quality control indicators


Extending the scholarly publication paradigm

Extending the scholarly publication paradigm

  • Standard data formats (CIF)

  • OAI-PMH

  • DOI, openURL

  • Standard metadata

  • Links to all data

  • Links to publication

  • Rights

  • Quality (checkCIF)


Biological macromolecules

Biological macromolecules

  • Similar considerations apply also to biological macromolecules, but community practice differs

  • The Worldwide Protein Data Bank (Rutgers PDB, MSD-EBI, PDBj) is the recognised deposition site(s) for protein structures

  • Need to capture ‘routine’ structural-genomics-derived structures

  • Policies for deposition of structure factors

  • Streamlined publication in Acta Cryst. Section F


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