Transcript Crystallography Journals Online

Visualisation of chemical data
Use cases for publication of crystal structures
Brian McMahon
Research & Development Officer
International Union of Crystallography
5 Abbey Square
Chester CH1 2HU
[email protected]
DataCite Summer Meeting, Hannover
7-8 June 2010
International Union of Crystallography
International Scientific Union
Publishes 8 research journals:
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Acta Crystallographica Section A: Foundations of
Crystallography
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Acta Crystallographica Section B: Structural
Science
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Acta Crystallographica Section C: Crystal
Structure Communications
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Acta Crystallographica Section D: Biological
Crystallography
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Acta Crystallographica Section E: Structure
Reports Online
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Acta Crystallographica Section F:Structural
Biology and Crystallization Communications
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Journal of Applied Crystallography
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Journal of Synchrotron Radiation
Publishes major reference work International
Tables for Crystallography (8 volumes)
Promotes standard crystallographic data file
format (CIF)
Crystal Structure reports - data-rich
scientific articles
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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
Raw data
Primary data
(image plate,
(structure factors)
diffractometer, film)
Derived data
(six-dimensional structural
model)
Structural data sets integral to publication
Every structural paper has an
associated data set (CIF)
These are free to access, even for
subscription journals
Hence accessible from browsable Table
of Contents (as well as from article)
User can download CIF data set
directly
Or visualise the structure interactively
in three dimensions
... using a standard view supplied by a
visualisation applet (Jmol) ...
... or a 'helper' application of the
reader's choosing (Mercury)
Enhanced figures
IUCr journals provide an authoring
toolkit for creating enhanced figures –
Data visualisations crafted by the author
(but allowing the reader to interact fully
with the data and create other
visualisations if desired)
The enhanced figure will appear (with
caption) as a normal figure in the
online journal; the PDF/print editions
will have an equivalent static view.
Additional views and interactive
features can be added by the author
if desired.
Data sources
The structural data (CIF) can
be uploaded to the journal
production office ...
... from the user's hard drive
(as part of the article
submission process) ...
... from an external
database using a known
accession code (e.g.
dn3141 for Crystallography
Journals Online, 3dez for
Protein Data Bank) ...
... or from a registered
data DOI (e.g.
10.2210/pdb3dez/pdb)
DOIs for crystallographic structures (1)
Article in IUCr Crystallography Journals Online
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Acta Cryst. (2010). C66, o274-o278 [ doi:10.1107/S0108270110015532 ] Different
hydrogen-bonding modes in two closely related oximes, G. Dutkiewicz, H. S.
Yathirajan, R. Ramachandran, S. Kabilan and M. Kubicki
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Describes structures of two molecules: 1-chloroacetyl-3-ethyl-2,6-diphenylpiperidin-4one oxime, C21H23ClN2O2 (at two distinct temperatures) and 1-chloroacetyl-2,6diphenyl-3-(propan-2-yl)piperidin-4-one oxime, C22H25ClN2O2
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IUCr identifier: dn3141 points to article and associated data sets
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DOI: 10.1107/S0108270110015532/dn3141sup1.cif
– DOI for data set (CrossRef) delivers data file directly
– One data file, three distinct data sets (file internally partitioned, data_I,
data_I100K, data_II)
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Other supplementary data sets available (processed experimental data)
– DOIs: 10.1107/S0108270110015532/dn3141Isup2.hkl etc.
– Separate data file for each of three refined structures
DOIs for crystallographic structures (2)
Macromolecular structure from Protein Data Bank
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Orotate phosphoribosyltransferase from Streptococcus mutans
PDB code: 3dez points to structure, associated data files, sequence, visualizations
etc.
DOI: 10.2210/pdb3dez/pdb
– DOI for data set (CrossRef) delivers data file directly
– One data file, one distinct data set (protein structure)
DOI of associated publication: 10.1107/S1744309110009243
– Acta Cryst. (2010). F66, 498-502 [ doi:10.1107/S1744309110009243 ] Structure
of orotate phosphoribosyltransferase from the caries pathogen Streptococcus
mutans, C.-P. Liu, R. Xu, Z.-Q. Gao, J.-H. Xu, H.-F. Hou, L.-Q. Li, Z. She, L.-F.
Li, X.-D. Su, P. Liu and Y.-H. Dong
PDB also archives structure factors (processed experimental data sets)
– One per refined structure
– No distinct DOI assigned
PDB does not (yet) archive primary data sets
– More than one per refined structure
DOIs for crystallographic structures (3)
Crystal structure in U. Southampton eCrystals repository
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2,2-dibutyl-1,3-propanediol
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eCrystals accession code: 643 points to structure, associated data files, visualizations
etc.
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DOI: 10.3737/ecrystals.chem.soton.ac.uk/643
– DOI assigned by CrossRef delivers portal page to all associated data files
– Portal links to raw data sets (archived off-site at STFC Atlas Facility)
– Portal links to derived information (chemical structure as CML files)
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DOI of associated publication:
– Publisher-assigned DOI if structure published in peer-reviewed journal
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unpublished
DOIs for crystallographic structures (4)
Unilever Cambridge Centre for Molecular Informatics / Project XYZ
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Proposal for JISC project (partners: IUCr, BioMedCentral, OKF)
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Explore data overlay journal: linking, validation, rights relating to crystal structures:
– Published (variety of commercial/society publishers)
– Unpublished (repositories, laboratory collections)
– Auto-generated annotation
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DOI:
– Strategy not yet elaborated. Probably includes:
– DOI assigned by DataCite delivers portal page to all associated data files
– Portal links to derived information (chemical structure as CML files)
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DOI of associated publication:
– Publisher-assigned DOI if structure published in peer-reviewed journal
–
unpublished
DOIs for crystallographic structures: summary
IUCr Crystallography Journals
Online
• DOI for article (CrossRef)
• Separate DOI for data set (CrossRef)
Protein Data Bank
• DOI for data set (CrossRef)
eCrystals / University of
Southampton
• DOI for data collection (CrossRef)
Unilever Cambridge Centre for
Molecular Informatics / Project
XYZ
• DOI for data collection? (DataCite)
* Need consistent protocols for retrieving data set
from larger data collection