Re: [dddwg] ESRF data policy article

Dear Andreas,

Sequence - absolutely yes. Crystallization conditions - I am not sure. You should have not only crystallization condition but also purification and protein production. During the data collection we access our LabDB system and rather push data from data collection/ processing to our system not to the synchrotron facility.

Please find enclosed our paper about data management.

Best regards

Wladek

On 2/7/2016 10:20 AM, Andreas Förster wrote:

Dear Gordon,

making the inclusion of protein sequence, crystallization conditions and the like mandatory in archived data would be a good idea.  At the most basic, it would make submission to the PDB much easier.  Every time I submit a structure, I scramble for these data that are always somewhere but never in one place.  If the diffraction data would tell me, I'd be ecstatic.  That said, the last thing I wanted to do when getting ready for beam time or at the synchrotron was filling in yet more boxes.  ISpyB already asks you to define project, crystal, etc, which I always found tedious, though in the end it made things flow more efficiently that if I just write pos1, pos2, etc, for the pins in the puck.

From my perspective as a representative of a detector manufacturer, it's important to hear what crystallographers at synchrotrons consider essential information to include in the metadata.  NeXus/HDF5 lets you store anything you want, but there needs to be an agreement among synchrotrons that is strictly adhered to.  We'd be more than happy to emphasize the metadata requirements during our commissioning presentations when we install a detector.

All best.

Andreas

On Sun, Feb 7, 2016 at 1:40 PM, Gordon LEONARD <leonard@esrf.fr> 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
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