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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.

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Data Curation in Crystallography: Publisher Perspectives

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  1. JISC Data Cluster Consultation Workshop CCLRC, Didcot, Oxon 10 October 2006 Data Curation in Crystallography: Publisher Perspectives

  2. 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

  3. Data that inform the discussion Raw data (image plate, diffractometer, film) Derived data (six-dimensional structural model) Primary data (structure factors)

  4. 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)

  5. 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

  6. 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

  7. 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)

  8. 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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