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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 <[log in to unmask]>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 [log in to unmask] > > -- 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: [log in to unmask] http://crg.ubc.ca/VanPetegem/