[3dem] Fwd: [ccp4bb] electron microscopy: where open access fails
Melissa Jurica
jurica at biology.ucsc.edu
Thu May 20 09:05:40 PDT 2010
An issue worth discussion from the ccp4 bulletin board:
Melissa Jurica
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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
http://www.mcd.ucsc.edu/faculty/jurica.html
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Begin forwarded message:
> From: Filip Van Petegem <filip.vanpetegem at GMAIL.COM>
> Date: May 18, 2010 4:47:58 PM PDT
> To: CCP4BB at JISCMAIL.AC.UK
> Subject: [ccp4bb] electron microscopy: where open access fails
> Reply-To: Filip Van Petegem <filip.vanpetegem at GMAIL.COM>
>
> 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.vanpetegem at gmail.com
> http://crg.ubc.ca/VanPetegem/
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