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Dear Kamil,
Please confirm where you plan to submit your Rovinj Workshop article which sounds an excellent contribution to me.
As a JAC Coeditor, now retired after the usual 9 years service, I would have been glad to take it forward to referees.
All best wishes,
John
Emeritus Professor of Chemistry John R Helliwell DSc_Physics
A new book resonating with the recent UN, UNESCO and IUCr International Year of Crystallography.
Dear John, dear All,
Thank you for all your emails, apologize for the delay in response. I am a bit concerned that the topic of my Rovinj article (metadata in high-pressure crystallography) is too crystallography-specific and will not attract attention of the general data journals'
readers. Your conclusion on the IUCr journals politics depicts quite a dismal situation.
Best regards,
Kamil
On 2015-12-04 09:00, John Helliwell wrote:
Hello Mitchell,
Sadly I won't be at the AsCA. I would have really liked to but had no budget, nor an invitation to then go seek a budget. I greatly enjoyed my visit to Kolkata in 2000.
I could be available by Skype on dec 7th, if you deem useful. If you could give me advance notice of questions you would like answering that would be efficient.
The reply from Andrew Allen was as Brian and I expected namely reflecting the new obsession with high impact leading therefore to a larger number, than reasonable, of rejections. Plus loose many of my newly formed data friends ! Bad for me, bad for IUCr.
I am inclined therefore to withdraw the proposal to JAC as the centralised focus for the Rovinj articles. IUCr journals is going to be anti community anti capacity building in future, new territory for us all. As an aside :- i used to spend many hours as editor
helping relatively inexperienced, low impact, authors with their submissions. I firmly believe they benefitted from that help but today those articles, polished, but lower impact would never get the light of day nor in future would those authors have that
kind of help to move forward in their science career growth. This will all have a serious effect on the global geography that IUCr journals will encompass in future.
Yours sincerely,
John
Dear Colleagues,
Are any members of the DDDWG planning to attend the AsCA meeting in Kolkata starting this weekend?
If so, please make contact with me and come to the lunchtime meeting on Dec 7 to discuss data deposition and other things.
Yours,
Mitchell Guss
On Friday, 4 December 2015, Coles S.J. < [email protected]> 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 <[email protected]<mailto:[email protected]>> on behalf of Wladek Minor <[email protected]<mailto:[email protected]>>
Reply-To: IUCr Working Group on Diffraction data Deposition <[email protected]<mailto:[email protected]>>
Date: Thursday, 3 December 2015 18:40
To: IUCr Working Group on Diffraction data Deposition <[email protected]<mailto:[email protected]>>
Cc: Marek Grabowski <[email protected]<mailto:[email protected]>>
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 [[email protected]<mailto:[email protected]>] on behalf of Michael Probert [[email protected]<mailto:[email protected]>]
Sent: 03 December 2015 15:05
To: [email protected]<mailto:[email protected]>
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
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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
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Professor Emeritus Mitchell Guss
School of Molecular Bioscience
Building G08
University of Sydney
NSW 2006
Australia
Phone:+61 (0)2 9351 4302
Fax: +61 (0)2 9351 5858
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