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Re: [dddwg] ESRF data policy article

Hi Wladek and Gordon,
Terms describing the experimental sample, crystallization conditions and the detailed molecularcomposition system of the sample are well described in existing data dictionaries developed under the auspicesof the IUCr and later extended by the PDB.     It would be most convenient if these data along withall of the methodological details could be captured consistent with this specification at this earlypoint in the experimental pipeline so they may be automatically incorporated into PDB depositions.
PDB would be very interested in sponsoring or participating in discussions or workshops to promotethe early encoding and standardization of these data.
Regards,
John

On 2/11/16 7:18 PM, Wladek Minor wrote:>> Dear Gordon,>> Yes, delay is entirely my fault.>> To update you, I have sent a list roughly 2 months ago. Tom have asked me for a few comments and  explanations and it took me too> long. Anyway, Tom has it and soon you can expect a list.>> I have missed a protein sequence that was proposed later.>>> Best regards>> Wladek>> On 2/7/2016 7:40 AM, Gordon LEONARD wrote:>> Hi Wladek,>>>> To answer your question, as far as I understand things (Andy G. will correct me if I'm wrong) the 3 year 'embargo' will be from>> the date the experimental data are collected.>>>> While I'm here, at the DDDWG working group workshop in Croatia I think you agreed to provide a draft of the metadata that should>> be archived along with raw data from MX experiments. Have you made any progress with this? Clearly, it would be nice if there were>> a standard description of a MX experiment that will allow reprocessing/re-analysis of raw data and it would be good if there could>> be agreement on this soon. As I said at the workshop, I think we could straightforwardly agree on a basic description of an>> experiment, but do we need to go further than this (i.e. include a full description of the sample including crystallisation>> conditions, amino acid sequence, etc)? IMO we should, but I might be in a minority in thinking this. Maybe we need another workshop!>>>> Talk to you soon,>>>> Yours,>>>> Gordon>>>> On 07/02/2016 10:48, Wladek Minor wrote:>>>>>> Dear Andy,>>>>>> This is great. You may also look into our server http://proteindiffraction.org.>>>>>> I have a question about 3 years. Should it be 3 years since the diffraction experiment or three years after PDB deposit ? In my>>> mind, data should available immediately when PDB deposit is released.>>>>>> Best regards>>>>>> Wladek>>>>>> On 2/7/2016 3:47 AM, Andy Gotz wrote:>>>> Dear John,>>>> thank you for your encouragement and support. The dddwg definitely played a role to get us this far and will continue to help>>>> defining standards for preserving data for diffraction experiments. We always cite the dddwg and its work when explaining the>>>> ESRF data policy. Thank you too and long live the dddwg!>>>>>>>> The policy foresees data being released by the PI before the 3 year embargo has expired. This is primarily to allow and>>>> encourage scientists to make the data publicly available as soon as they publish their results. The policy does not foresee the>>>> specific case of anonymous access for referees before the PI has made the data public and/or the 3 year embargo period has>>>> expired. If referees want access to the data beforehand we think it is up to the PI to decide this. The PI can then add the>>>> referee to the experimental team thereby granting them access to the data.>>>>>>>> The preferred data format for archived data will be HDF5 as container and Nexus as the ontology. Conversion programs will>>>> convert HDF5/Nexus to other formats if required.>>>>>>>> Kind regards>>>>>>>> Andy>>>>>>>> On 07/02/2016 08:54, John Helliwell wrote:>>>>> Dear Andy,>>>>> Please also accept my Hearty congratulations on this very important development.>>>>>>>>>> The access to specific data sets by referees, an editor and eventually readers of an article relying on those data will be via>>>>> your registration process mentioned in the policy I assume? Very often this will be before 3 years have elapsed since the>>>>> measurements; will (registered) access be allowed during those first three years? (referees of course may well need to be>>>>> anonymous to conform with a given journal's policy and/or their own wishes.)>>>>>   Like Tom, I put out a tweet yesterday evening. One immediate query that has come up concerned data format (Nexus was asked>>>>> about). If you let me have your answer (in less than 140 characters) I will reply for you if you wish. Or, with your>>>>> permission, I can let the person who raised it know that you are the person to contact.>>>>>>>>>> Hearty congratulations once again.>>>>> John>>>>>>>>>>>>>>>>>>>> Emeritus Prof of Chemistry John R Helliwell DSc_Physics>>>>> https://www.crcpress.com/Perspectives-in-Crystallography/Helliwell/9781498732109>>>>> A new book which resonates with the recent UN, UNESCO and IUCr International Year of Crystallography.>>>>>>>>>> On 6 Feb 2016, at 17:31, "Andy Gotz" <andy.gotz@esrf.fr> wrote:>>>>>>>>>>> Dear All,>>>>>>>>>>>> FYI an article on the ESRF data policy is now online:>>>>>>>>>>>> http://www.esrf.eu/home/news/general/content-news/general/esrf-takes-the-helm-in-saving-data.html>>>>>>>>>>>> It will be presented at the ESRF Users meeting next week.>>>>>>>>>>>> Andy>>>>>> _______________________________________________>>>>>> dddwg mailing list>>>>>> dddwg@iucr.org>>>>>> http://mailman.iucr.org/cgi-bin/mailman/listinfo/dddwg>>>>> _______________________________________________>>>>> dddwg mailing list>>>>> dddwg@iucr.org>>>>> http://mailman.iucr.org/cgi-bin/mailman/listinfo/dddwg>>>>>>>> _______________________________________________>>>> dddwg mailing list>>>> dddwg@iucr.org>>>> http://mailman.iucr.org/cgi-bin/mailman/listinfo/dddwg>>>>>>> _______________________________________________>> dddwg mailing list>> dddwg@iucr.org>> http://mailman.iucr.org/cgi-bin/mailman/listinfo/dddwg>
-- John Westbrook, Ph.D.RCSB, Protein Data BankRutgers, The State University of New JerseyDepartment of Chemistry and Chemical Biology174 Frelinghuysen RdPiscataway, NJ 08854-8087e-mail: john.westbrook@rcsb.orgPh: (848) 445-4290 Fax: (732) 445-4320_______________________________________________dddwg mailing listdddwg@iucr.orghttp://mailman.iucr.org/cgi-bin/mailman/listinfo/dddwg

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