[3dem] Outcomes of an informal discussion at the 2012 3DEM GRC meeting about deposition requirements for tomographic data

[outreach at emdatabank.org]

Dear all, 

At the 2012 3DEM GRC, EMDataBank organized an informal discussion session on
tomography deposition. We (EMDataBank) would like to thank the ~20 meeting
participants for a lively and productive discussion that resulted in
consensus on the following issues: 

1.      For publications describing sub-tomogram averages, map deposition to
EMDB should be mandatory. 

2.      For publications describing tomographic reconstructions without
sub-tomogram averaging, deposition of representative tomographic
reconstructions is strongly recommended but should not be mandatory at this
stage. The reason for this is that there are cases where the deposition of
all tomographic reconstructions associated with a publication (or even just
the reconstructions associated with the images included in the publication)
would be impractical. 

3.      Validation of tomographic reconstructions is still in its infancy
and it is therefore premature to consider concrete actions. Instead,
EMDataBank should focus on encouraging deposition. 

4.      EMDataBank should prepare a recommended deposition policy for
journals clarifying the guidelines for tomography deposition and circulate
it to the wider EM community for comments. 

EMDataBank has prepared the following recommended deposition policy for
journals publishing 3DEM structural results, based on the current PNAS
policy: 

"For papers describing structures of biological macromolecules from electron
microscopy experiments including sub-tomogram averaging, the 3D maps must be
deposited at either of the EMDB deposition sites at EMBL-EBI PDBe (UK) or
RCSB PDB (USA) (accessible through emdatabank.org). For electron tomographic
studies that do not include sub-tomogram averages, the deposition of
representative tomographic reconstructions to an EMDB deposition site is
strongly recommended. In both cases, the EMDB accession codes should be
included in the manuscript." 

  

We would like to hear the views of the wider EM community on the suggested
deposition guidelines for tomography listed above as well as the draft
deposition-policy text. Your feedback is important to us as the guidelines
will inform EMDataBank policy and we will attempt to achieve widespread
adoption of the recommended deposition policy by the relevant journals. 

  

We would be grateful if you could discuss these issues in your labs and
forward this message to colleagues who may not subscribe to 3DEM. If you
would prefer not to respond to the 3DEM mailing list, please feel free to
mail us directly at help at emdatabank.org. The deadline for feedback is 29
June 2012, and we will post a summary of the feedback received on
emdatabank.org. Many thanks in advance! 

  

On behalf of EMDataBank - Ardan Patwardhan and Cathy Lawson 

 

 

 

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