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

Thu Apr 30 15:33:06 PDT 2015

At the risk of merely echoing some of Steve's comments, I would like to 
say that while journals will not necessarily use your recommended 
reviewers, they will almost always honor your reasonable requests to 
exclude certain reviewers. This undercuts any reason to be paranoid, 
unless you think that there are many people who will unethically use 
your map.
Ed

On 4/30/15 6:13 PM, Ludtke, Steven J wrote:
> 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 ofsome 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 ofsubmission 
>>>> for the purposes of evaluating the manuscript.Peer-reviewersmay be 
>>>> askedto 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>
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> 3dem mailing list
>>>> 3dem at ncmir.ucsd.edu
>>>> https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem
>>>
>>> -- 
>>> __________________________________________________________________
>>>
>>> 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
>>> __________________________________________________________________
>>> _______________________________________________
>>> 3dem mailing list
>>> 3dem at ncmir.ucsd.edu <mailto:3dem at ncmir.ucsd.edu>
>>> https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem
>>
>> _______________________________________________
>> 3dem mailing list
>> 3dem at ncmir.ucsd.edu <mailto:3dem at ncmir.ucsd.edu>
>> https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem
>
>
>
> _______________________________________________
> 3dem mailing list
> 3dem at ncmir.ucsd.edu
> https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem

-- 
Edward H. Egelman, Ph.D.
Professor
Dept. of Biochemistry and Molecular Genetics
University of Virginia

President
Biophysical Society

phone: 434-924-8210
fax: 434-924-5069
egelman at virginia.edu
http://www.people.virginia.edu/~ehe2n

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ncmir.ucsd.edu/pipermail/3dem/attachments/20150430/23c90f37/attachment-0001.html>