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Re: [dddwg] ESRF data policy article


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
-- Dr. Wladek MinorProfessor of Molecular Physiology and Biological PhysicsPhone: 434-243-6865Fax: 434-982-1616http://krzys.med.virginia.edu/CrystUVa/wladek.htm

US-mail address:Department of Molecular Physiology and Biological PhysicsUniversity of VirginiaPO Box 800736, Charlottesville, VA 22908-0736
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