[3dem] Fwd: [ccp4bb] electron microscopy: where open access fails

Melissa Jurica jurica at biology.ucsc.edu
Thu May 20 09:06:38 PDT 2010


Melissa S. Jurica, Ph.D.
Molecular, Cell & Developmental Biology
Center for Molecular Biology of RNA
UC Santa Cruz
1156 High Street
Santa Cruz, CA 95064

Office: 251 Sinsheimer Labs
Lab: 237 Sinsheimer Labs
Office phone (831) 459-4427
Lab phone (831) 459-2463
Fax (831) 459-3139


Begin forwarded message:

> From: Filip Van Petegem <filip.vanpetegem at GMAIL.COM>
> Date: May 20, 2010 8:30:57 AM PDT
> Subject: Re: [ccp4bb] electron microscopy: where open access fails
> Reply-To: Filip Van Petegem <filip.vanpetegem at GMAIL.COM>
> Dear Cathy/EMDATABANK team:
> It is hard to comprehend the option for keeping maps on hold for up  
> to 2 years.  It seems any depositor would do this for pure selfish  
> reasons: keep the data to themselves, don't allow anybody to verify  
> the data for a long time, and have the exclusive right to do  
> experiments with the maps. For example, this would allow the  
> depositor to be the only one perform docking experiments with any  
> partial crystal structure for 2 years, and also these experiments  
> wouldn't be falsifiable for a period of 2 years (!).
> Comparing this with crystallography: one would keep a crystal  
> structure of a good drug target 'on hold' for 2 years, thus not  
> allowing anybody to use it to start rationally designing new drugs  
> (the success rate aside for this matter).
> In scientific terms, two years is 'huge'.  It is in this time frame  
> that a new theory can be postulated by one, and then shot down by  
> ten other papers.  It is 40% of the time frame of an NIH ROI1  
> grant, and 66% of a typical Canadian CIHR grant. When it comes to  
> cryoEM and crystal structures of important therapeutic targets,  
> delaying the field for 2 years will ultimate cost lives.
> In the end, journal editors should create firmer and waterproof  
> policies like those implemented for crystal structures, such as not  
> allowing publication until the data are in the 'hold for  
> publication' status. Some journals already have the clear policy of  
> requiring deposition of the cryoEM maps, but the 2 year hold is  
> currently a big loophole.  Many more journals, however, don't  
> require the deposition of maps at all.  Of course it would help if  
> the EMDB didn't allow for these loopholes...
> Sincerely,
> Filip Van Petegem
> On Thu, May 20, 2010 at 7:16 AM, Cathy Lawson  
> <cathy.lawson at rutgers.edu> wrote:
> sent on behalf of the EMDATABANK.org team:
> The EM Databank (EMDB, http://www.emdatabank.org/) is a resource  
> for the archival deposition and retrieval of EM maps and associated  
> metadata. It was established in 2002 by the European Bioinformatics  
> Institute (EMBL-EBI, UK), and is now run jointly by EBI, the  
> Research Collaboratory for Structural Bioinformatics (RCSB, USA),  
> and the National Center for Macromolecular Imaging (NCMI) at Baylor  
> College of Medicine.
> Following the model of the wwPDB, development of EMDB policies and  
> procedures is community-driven. The resource is advised by a panel  
> of leading experts. This fall, an Electron Microscopy Validation  
> Task Force (EM VTF) will be convened to make recommendations as to  
> how best to assess the quality of both maps and models that have  
> been obtained from cryo-EM data.  Its recommendations will form the  
> basis for a validation suite that will be used for maps and models  
> deposited in the appropriate databases (EMDB and PDB).
> As seen by the history of the PDB, journal requirements can greatly  
> influence data deposition. For articles reporting the results of  
> electron microscopy studies, the rate of EM map deposition is  
> higher for journals that have well-defined and consistently- 
> enforced policies than for journals without deposition  
> requirements.  We have recently contacted journals that publish EM  
> studies to encourage them to include a deposition policy for EM  
> structural data in the instructions to Authors, and we are  
> continuing to follow up with them.
> Currently, depositors may choose to release deposited data  
> immediately, upon publication (selected by the majority), after 1  
> year, or after 2 years. The 1 and 2 year holds are intended to  
> encourage EM scientists to deposit maps by providing a time period  
> in which they can perform additional studies/analyses before the  
> map is made public.  Based upon community feedback, the option to  
> hold a map for 4 years was retired in 2008.
> Questions about the EMDB may be sent to help at emdatabank.org.
> -- 
> Filip Van Petegem, PhD
> Assistant Professor
> The University of British Columbia
> Dept. of Biochemistry and Molecular Biology
> 2350 Health Sciences Mall - Rm 2.356
> Vancouver, V6T 1Z3
> phone: +1 604 827 4267
> email: filip.vanpetegem at gmail.com
> http://crg.ubc.ca/VanPetegem/

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