[3dem] sharing em maps during peer-review process

Ludtke, Steven J sludtke at bcm.edu
Thu Apr 30 15:13:39 PDT 2015


I'm not sure if endless echoing is going to be that worthwhile, but I'll add that I have been involved in a couple of reviews where not only were final maps required, but a reviewer (not me) actually requested the raw data (or a portion of the raw data) involved in the reconstruction! I know I am not alone in seeing cases like this. Admittedly in these cases, the editor did seem a bit taken aback, but still followed through after discussing with the author.

I cannot see that one has any ground to stand upon in refusing to submit their final map to reviewers. In theory the paper should encompass the entire results of the study. The fact that it isn't possible to fully represent the data in the publication itself doesn't negate the philosophical point. Either you are ready to release your result to the world or you aren't. Publishing isn't about hiding things, it's about spreading your new knowledge as widely as possible. Given the requirement to deposit to the EMDB, at most this gives the reviewer a brief lead on general public access. The 'hold past publication' policy in the databases is transitioning out anyway. The excuse that "it took me 3 years to solve the structure and it will take me another 2 years to really dissect the map" is fading as cryoEM is becoming a higher throughput technique. The idea that you so mistrust your colleagues that you would require an MTA for the review process is completely ludicrous. If there are IP concerns about a particular result, you should not publish it until you are ready to share with the world. I, for one, have no problem in forgoing my anonymity in the review process, as journals like eLife promote, but I can at least understand the value in being permitted to remain anonymous. If there are specific colleagues that you fear will misuse your data, you should identify them in the cover letter to the editor with your reasoning, and trust the ethics of the editor.

On Apr 30, 2015, at 4:46 PM, Gabriel Lander <glander at scripps.edu<mailto:glander at scripps.edu>> wrote:

I would like to echo Eva & Ed’s comments (I am also NOT a reviewer).
Given that the EM field hasn’t really settled on a robust methodology to statistically assess the accuracy & validity of a density (yes we have gold standard FSC, local resolution plots, tilt-pair validation, etc. but these are not 100% foolproof, & there are ways to inflate resolution nonetheless), we generally rely on our eyes to ascertain the quality of map.

I’m sure your density doesn’t fall into this category of “inaccurate” structure determination, so I’m curious what you think a reviewer might do with your density to misuse it?
I agree with Ed that all densities should be uploaded with a submitted manuscript, and I am happy to do this for any manuscripts we send out.
-gabe


On Apr 30, 2015, at 2:16 PM, Eva Nogales <enogales at lbl.gov<mailto:enogales at lbl.gov>> wrote:

Hi Friedrich,

We got the same request and we provided the map and model as a Chimera session to the editor and reviewer. I understand your point, but we have to trust the system and understand where the reviewers may be coming from. We do know of more than one example where having had such access  may have precluded publication of some really terrible structures. It will be interesting to hear what others think (and I have no doubt the reviewer(s) that asked for your and our maps is/are within the list reading this email...)

Eva

On 4/30/15 1:49 PM, Friedrich Foerster wrote:
dear colleagues,

i would be interested in experiences / suggestions / views of others in the field on  the following issue that may be of interest to many of us:
the editor of our manuscript forwarded the request of a peer-reviewer to access the cryo-em map of our beloved complex. this has never happened to us, but to our surprise the editor did not consider the request to be unusual.
of course, we share the point that the map would be of great help in judging the interpretation of the data. however, we also feel very uncomfortable sending the condensed result of lengthy research to an anonymous colleague, who could theoretically make considerable misuse of it. nevertheless, the policy of the journal seems to let us little choice: "Supporting data must be made available to editors and peer-reviewers at the time of submission for the purposes of evaluating the manuscript. Peer-reviewers may be asked to comment on the terms of access to materials, methods and/or data sets".
in any case we would be curious whether others indeed got similar requests and how they dealt with it. a good solution for (paranoid?) people like us could be a good web-based viewer that lets others view our map, but i would not know of such a tool.

Thanks

Friedrich

--
Dr. Friedrich Foerster
Max-Planck Institut fuer Biochemie
Am Klopferspitz 18
D-82152 Martinsried

Tel: +49 89 8578 2632
Fax: +49 89 8578 2641

www.biochem.mpg.de/foerster<http://www.biochem.mpg.de/foerster>




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--
__________________________________________________________________

Eva Nogales
Howard Hughes Medical Institute
Molecular and Cell Biology Department
QB3, Stanley Hall 708C
University of California, Berkeley
Berkeley, CA 94720-3220

Phone: (510) 642-0557           Fax: (510) 666-3336
URL: cryoem.berkeley.edu<http://cryoem.berkeley.edu/>
(510) 666-3334          Teresa Tucker, Assistant to Eva Nogales

Professor, UC Berkeley and Lawrence Berkeley Natl. Lab
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