2017-10-18 : 5247 EMDB map entries, 1838 PDB coordinate entries PDBe | RCSB    

One-stop shop for 3DEM deposition and retrieval

 

Proposed Deposition Requirements for Tomographic Data

Tomographic data deposition was the main topic of an informal afternoon meeting at the 2012 3DEM GRC that drew ~20 conferees.

There was general consensus among the group regarding the following points:

  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@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!