Re: [ccp4bb] electron microscopy: where open access fails
Dear Filip, CCP4BB, 3DEM, and PDB-L list members, Thank you for your enthusiastic showing of community support for mandatory deposition of cryoEM maps to EMDB and for their timely release. The two year hold is available to EMDB depositors for just one practical reason: it encourages deposition of maps that we would probably otherwise not be getting at all (and those experiments would thus never be falsifiable). Until journals and major funding agencies make deposition and immediate release mandatory, we have to compromise. A large number of petition signatures ( http://www.petitiononline.com/cryoEM/petition.html ) will certainly help us to solidify our case. It is easy to forget that it was not until 1989 (17 years after the PDB began collecting X-ray structures) that community-set guidelines were published for X-ray crystallography coordinate deposition, and several more years before the journals required deposition as a prerequisite for publication. Structure factor deposition only became mandatory in 2008. These policies emerged from cooperative action by the community of experimentalists and interestingly included a petition that was led by Fred Richards. The same process will be effective for the EM community. Sincerely, The EMDataBank.org team http://emdatabank.org
Re: [ccp4bb] electron microscopy: where open access fails
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 h...@emdatabank.org.
Re: [ccp4bb] electron microscopy: where open access fails
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.law...@rutgers.eduwrote: 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 h...@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.vanpete...@gmail.com http://crg.ubc.ca/VanPetegem/
Re: [ccp4bb] electron microscopy: where open access fails
Dear crystallographers, For those of you who have shared personal frustration with cryoEM map availability, or for those of you who would simply like to see science proceed as it should, here's your opportunity to sign an on-line petitition. Please feel free to send the link below to any of your colleagues. More signatures = more pressure. http://www.petitiononline.com/cryoEM/petition.html Sincerely, Filip Van Petegem -- 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.vanpete...@gmail.com http://crg.ubc.ca/VanPetegem/
[ccp4bb] electron microscopy: where open access fails
Dear colleagues, whereas data sharing for most crystallographers appears to be a no-brainer, making coordinates and (most of the time, hopefully) structure factors available, it seems the electron microscopists are drastically lagging behind when it comes to making data available. Many cryoEM structures are still being published without the corresponding maps being deposited in the EM database. In one particular case, I was interested in looking at a cryoEM map from a paper published in a well-renowned open access journal starting. The paper contains the EMDB accession codes for the maps, but these maps appear to be 'on hold' since over a year. Enquiry with the authors delivered a firm 'no' in releasing the maps: they claim it is OK to keep the maps on hold for 2 years, simply because the EMDB gives the option to do so. A further enquiry with the journal editors led to no avail: despite the clear journal policy on sharing both manuscripts and data, they were also unable to force the authors to release their maps, now ~13 months after publication of the paper. The fact that this was in an open access journal makes this all the more shocking. It is striking to see how much still has to be done to lift the cryoEM world up to the same standards as the crystallographic community (when it comes to sharing data, at least). Structures can simply be published without anybody being able to check the validity, let alone use it for obvious experiments such as docking crystal structures, integrative protein structure modeling, etc. With many structural targets going towards bigger and more challenging, combining cryoEM data with crystal structures is going to become more and more important. What can we, crystallographers, do to stimulate data-sharing in the cryoEM world? (My apologies to the cryoEM people on this bulletin board: if you have been making your maps available, you'll agree that clearly not everybody does...) Filip Van Petegem -- 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.vanpete...@gmail.com http://crg.ubc.ca/VanPetegem/
Re: [ccp4bb] electron microscopy: where open access fails
When X-ray crystallographers not so many years ago thought they are the salt of the earth, of science and then some (well, some believe so to this date), the same attitude prevailed (data holds). Once every person with access to Google does it, that secrecy slowly disappears. What also helps is a few major fups, which promotes community response by those who have nothing to hide. Fups tend to happen at the transition from expert science to Google science. EM is probably not there yet. So, talk to you colleagues, question every structure, and make the argument that science without data is non-falsifiable in Popper's sense and thus en par with quackery and superstition. That should make you a lot of friends (or at least it will draw a response). Cheers, BR From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Filip Van Petegem Sent: Tuesday, May 18, 2010 4:48 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] electron microscopy: where open access fails Dear colleagues, whereas data sharing for most crystallographers appears to be a no-brainer, making coordinates and (most of the time, hopefully) structure factors available, it seems the electron microscopists are drastically lagging behind when it comes to making data available. Many cryoEM structures are still being published without the corresponding maps being deposited in the EM database. In one particular case, I was interested in looking at a cryoEM map from a paper published in a well-renowned open access journal starting. The paper contains the EMDB accession codes for the maps, but these maps appear to be 'on hold' since over a year. Enquiry with the authors delivered a firm 'no' in releasing the maps: they claim it is OK to keep the maps on hold for 2 years, simply because the EMDB gives the option to do so. A further enquiry with the journal editors led to no avail: despite the clear journal policy on sharing both manuscripts and data, they were also unable to force the authors to release their maps, now ~13 months after publication of the paper. The fact that this was in an open access journal makes this all the more shocking. It is striking to see how much still has to be done to lift the cryoEM world up to the same standards as the crystallographic community (when it comes to sharing data, at least). Structures can simply be published without anybody being able to check the validity, let alone use it for obvious experiments such as docking crystal structures, integrative protein structure modeling, etc. With many structural targets going towards bigger and more challenging, combining cryoEM data with crystal structures is going to become more and more important. What can we, crystallographers, do to stimulate data-sharing in the cryoEM world? (My apologies to the cryoEM people on this bulletin board: if you have been making your maps available, you'll agree that clearly not everybody does...) Filip Van Petegem -- 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.vanpete...@gmail.com http://crg.ubc.ca/VanPetegem/
