Discussion List Archives

[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]

Re: [dddwg] Initiation of formal proposal resulting fromdiscussions at the DDDWG satellite meeting of the ECM Croatia

Simon,I fully agree. There is no catch 22 - only a delay between the time the doi is minted and the time the data is made public. This does not change the doi or its citation in the paper. The ILL mints the doi's as soon as the experiment starts and emails it to the PI and collaborators e.g. http://doi.ill.fr/10.5291/ILL-DATA.9-11-1654Andy
On 03/12/2015 19:57, Coles S.J. wrote:> Wladek,>> On point 3 – DOI citation…>> It is up to the individual to ascribe a DOI to a dataset – so at the point of writing a manuscript, in theory, you know what it will be. The DOI only becomes active when it is minted i.e. DataCite (or whoever) are told the identifier and its associated metadata and they put it in their public registry. A DOI would generally point to a landing page – this would be the HTML jump off page of your archive (or similar). Its OK for the data behind the landing page to be embargoed until the point when someone wishes to lift the embargo e.g. on acceptance of a paper.>> The only catch 22 I now see is if you wish referees of the paper to see the raw data when they are reviewing. I have a system where a record in an archive has a secure ‘back door’ link i.e. It can be embargoed but the owner of the record can hand the link out e.g. to a journal, and they can access the dataset.>> All this involves some architecture, a certain amount of procedural change/addition, and some more effort on the shoulders of the researcher, but it does make the catch 22 surmountable…>> Simon.>> Simon Coles.> Associate Professor & Director, UK National Crystallography Service.> Chemistry, Faculty of Natural and Environmental Sciences,> University of Southampton.> Southampton, SO17 1BJ. UK.> +44(0)2380596721> Staff Page: http://www.soton.ac.uk/chemistry/about/staff/sjc5.page> NCS: http://www.ncs.ac.uk<http://www.ncs.ac.uk/> <http://www.ncs.ac.uk/> | Southampton Diffraction Centre: http://www.soton.ac.uk/sdc> ResearcherID: http://www.researcherid.com/rid/A-1795-2009 | ORCID: http://orcid.org/0000-0001-8414-9272>>>> From: dddwg <dddwg-bounces@iucr.org<mailto:dddwg-bounces@iucr.org>> on behalf of Wladek Minor <wladek@iwonka.med.virginia.edu<mailto:wladek@iwonka.med.virginia.edu>>> Reply-To: IUCr Working Group on Diffraction data Deposition <dddwg@iucr.org<mailto:dddwg@iucr.org>>> Date: Thursday, 3 December 2015 18:40> To: IUCr Working Group on Diffraction data Deposition <dddwg@iucr.org<mailto:dddwg@iucr.org>>> Cc: Marek Grabowski <marek@iwonka.med.virginia.edu<mailto:marek@iwonka.med.virginia.edu>>> Subject: Re: [dddwg] Initiation of formal proposal resulting from discussions at the DDDWG satellite meeting of the ECM Croatia>>> Dear All,>> Some clarifications>> 1. Frame  formats:>> As I wrote to Herbert, there is no single CBF format - beamlines create various modifications. Some companies that distribute Detectors also created their own frame format. Tom Terwilliger and I  are working on minimum metadata header that would allow to process datasets. If this header would be add to every  frame format, such a data usually can be  process easily regardless the information that is in other part of the header.>> 2. doi>> We now have over 2800 publicly available diffraction experiments (around 300 are in pipeline). As of today, we are starting to assign doi. There are several problems related to it. For examle:> Once doi is assigned, it can not be removed or modify. What one should do when PDB depositor changes the title. We can not change doi. We will follow PDB approach to it.>> 3. doi citations>> People will not use doi citations in their original paper because doi data have to be public and this can happen only when paper is already publish. I do believe that we have catch 22 here.>> Best regards>> Wladek>> On 12/3/2015 12:00 PM, John Helliwell wrote:> Dear Mike,> Many thanks for bringing your proposal about area detector raw data image formats, that you aired in Rovinj, forward.> You mention imgcif and HDF5/NeXus explicitly and so we invite Herbert Bernstein, as chair of that work, to respond directly to your proposal and its possible practical implementation.> Thankyou,> John and Brian> PS Just one, admittedly very specific detail, whilst the bulk of MX data is collected at the synchrotron (estimated at around 90%) we believe that about 95% of 'small molecule' single crystal are detector data is measured on home lab set ups.>> Emeritus Prof of Chemistry John R Helliwell DSc_Physics> Perspectives in Crystallography<https://www.crcpress.com/Perspectives-in-Crystallography/Helliwell/9781498732109>>>> ________________________________> From: dddwg [dddwg-bounces@iucr.org<mailto:dddwg-bounces@iucr.org>] on behalf of Michael Probert [Michael.Probert@newcastle.ac.uk<mailto:Michael.Probert@newcastle.ac.uk>]> Sent: 03 December 2015 15:05> To: dddwg@iucr.org<mailto:dddwg@iucr.org>> Subject: Re: [dddwg] Initiation of formal proposal resulting from discussions at the DDDWG satellite meeting of the ECM Croatia>>> Dear All,>>> following a lively and entertaining discussion at this year's DDDWG satellite meeting in Croatia, I feel that we should attempt to formalise some of the thoughts discussed. Therefore I enclose a starting point for discussion in a proposal at the bottom of this email. I feel very strongly about the need for advancement in this area and that the time is absolutely correct to initiate this. It has recently been pointed out that some institutions are already archiving raw data and defining sensible protocols for this seems incredibly sensible if not an absolute necessity for the longevity of such projects.>>> Please feel free to comment on the outline below - I would hope that we could come to some agreed position that could then be taken forward by the group leaders as representative of our collective feelings on the issue of data storage, usefulness and to a certain extent future proofing.>>> I hope that I have managed to convey my ideas clearly and that the proposal makes sense. I am certain that there are aspects that need clarification and am equally certain that a large degree of finessing may be required before this can be taken to the next step. However we must start somewhere and condensing ideas from the meeting seems a good place to start.>>> Many thanks for your time, bye for now>>> Mike>>> The need for fully archived data is becoming more apparent and the> volume of said data is becoming ever greater. One of the larger> hurdles to this process is that for the data archived to be useful it> must be stored in a format that allows other users the ability to> interact with it. Some years ago the idea of imgCIF was created, but> for various reasons instrument manufacturers were reluctant to adapt> to this format. Since then with the advent of newer detector> technologies there has been a small explosion in the number and> variety of frame formats that are currently in use. It now seems a> daunting uphill task to convince all developers to rewrite their> firmware to output a common image format, therefore an alternative> must be found. As a community we currently archive data (positions and> structure factors) in a common format - CIF. There is no reason why> this philosophy would not work for the raw data as well. Users> currently convert all of their processed data into CIF format for> publication, therefore I put it to the DDDWG that one sensible way> forward would be to have users archive their raw data in a common format> (be that imgCIF or HDF5/NeXus) at the point of submission. There are> currently image conversion utilities available for some image formats> and it would not take a large investment of time to generate these for> all users; indeed, I am sure nearly all of these are written in various> places around the world. If the conversion is lossless and all> information on the experimental setup is maintained then there is no> reason for any degradation of data, but there is the huge advantage> that this information would then be of use to everyone for> reinvestigation or authentication protocols. I believe this results in> one moderately sized problem in deciding which format is the best to> use for archiving. This problem can be approached in different ways> although there is, I believe, a simple and pragmatic answer; the> majority of raw data is now produced at synchrotrons due to the> technologies employed - therefore we should take the direction from>> them as they are mostly working towards something common in format.>>>>> Dr Michael R. Probert> Head of Crystallography> Lecturer in Inorganic Chemistry> School of Chemistry> Newcastle University> Bedson Building> Newcastle upon Tyne> NE1 7RU>> tel: +44(0) 191 208 6641> fax: +44(0) 191 208 6929>>>> _______________________________________________> dddwg mailing list> dddwg@iucr.org<mailto:dddwg@iucr.org>http://mailman.iucr.org/cgi-bin/mailman/listinfo/dddwg>>> --> Dr. Wladek Minor> Professor of Molecular Physiology and Biological Physics> Phone: 434-243-6865> Fax: 434-982-1616> http://krzys.med.virginia.edu/CrystUVa/wladek.htm>>> US-mail address:> Department of Molecular Physiology and Biological Physics> University of Virginia> PO Box 800736, Charlottesville, VA 22908-0736>> Fed-Ex address:> Department of Molecular Physiology and Biological Physics> 1340 Jefferson Park Avenue> University of Virginia> Charlottesville, VA 22908>> ----> _______________________________________________> dddwg mailing list> dddwg@iucr.org> http://mailman.iucr.org/cgi-bin/mailman/listinfo/dddwg
_______________________________________________dddwg mailing listdddwg@iucr.orghttp://mailman.iucr.org/cgi-bin/mailman/listinfo/dddwg

Reply to: [list | sender only]
International Union of Crystallography

Scientific Union Member of the International Science Council (admitted 1947). Member of CODATA, the ISC Committee on Data. Partner with UNESCO, the United Nations Educational, Scientific and Cultural Organization in the International Year of Crystallography 2014.

International Science Council Scientific Freedom Policy

The IUCr observes the basic policy of non-discrimination and affirms the right and freedom of scientists to associate in international scientific activity without regard to such factors as ethnic origin, religion, citizenship, language, political stance, gender, sex or age, in accordance with the Statutes of the International Council for Science.

Useful links