[Cod-bugs] Information request for academic purposes

Tue Apr 16 15:06:14 EEST 2024

Dear Antony,

thank you for your e-mail and for the interest in the COD! Below I'll 
answer your questions:

On 2024-04-12 15:07, Antony Fornes wrote:
>
> Hello,
>
> We are currently conducting a study on Crystallography Open Database 
> (COD) to expand our inventory of available research data repository 
> solutions. This study, undertaken as part of Université Côte d'Azur, 
> aims to create a guide to assist our research community in identifying 
> the most suitable services for their needs.
>
> We have a few questions :
>
> Can the depositor restrict access to his files? If so, is this 
> restriction limited to an embargo?
>
Yes. The default embargo period is 6 months, with the possibility to 
extend it in 6 month additional periods.

During the embargo period, only the formula, compound name and the cell 
constants of the crystal displayed publicly in the database, but not the 
atomic coordinates and other data.

Currently, we do not enforce the end of embargo, trusting the depositors 
to declare their data published and open. In future this may (should :) 
) change, but in any case we will send information messages to the 
depositors and corresponding authors about the decision to open the data 
or extend the embargo, and make sure that all stakeholders have time and 
opportunity to react.

> Does the repository support the upload of large files? If so, is there 
> a limit to the size or number of files that can be uploaded?
>
We can accept large files where the size is limited by the underlying 
file system. One of the ways to do it it to use a good old anonymous FTP 
server. This upload however is not automatic, please contact us if you 
plan to deposit large files (e.g. original diffraction images). In this 
way, for example, derived databases are uploaded to the COD [1].

In case you would like to deposit the raw diffraction images 
systematically, we can add links to other repositories (such as XRDa 
[2]), provided they have stable, unique, persistent identifiers 
resolvable on-line. There are also plans to host raw diffraction data in 
Vilnius University, which are under development.

> Does the repository offer medium-term (5-10 years) data preservation 
> for distribution purposes? Furthermore, does it provide long-term 
> archiving services?
>
The aim of the COD is to maintain open access to crystallographic data 
for as long as it is needed by the community. Last year we proudly 
celebrated 20 years on-line, so yes, /de facto/ we can and do provide 
access to the data for more than 2 decades. There are plans to expand 
and extend the COD into the future, and we have contingency plans such 
as mirrors in other countries (Spain) in case of emergency. So the 
answer to both of your questions is yes, with understanding that here 
might be /force majeure/ circumstances such as war that might make 
carrying out the existing plans difficult...
>
> Does the repository automatically generate a citation with the data 
> references ?
>
Not yet but we have recommendations of how to do this (they are planned 
to be included into the International Table of Crystallography) [3]. The 
COD provides all necessary metadata to create such citations.
>
> Thank you very much for your attention to our questions.
>
HTH,

Sincerely yours,
Saulius

Refs.:

[1] PANalytical (2023) HighScore (Plus) COD database. URL: 
http://www.crystallography.net/cod/archives/2023/PANalytical/ [accessed 
2024-04-16T14:41+03:00]

[2] Xtal Raw Data Archive Maintainers (2020). Xtal Raw Data Archive. 
URL: https://xrda.pdbj.org/ [accessed: 2023-07-16T23:53+03:00]

[3] Gražulis, S. (2016) COD data citation. In the presentation "The 
Crystallography Open Database" at the OpenCon 2016, Kaunas, Lithuania 
(slides 18 & 19). URL: 
http://www.crystallography.net/cod/archives/2016/slides/2016-Kaunas-OpenCon2016/slides.pdf 
[accessed 2024-04-16T14:52+03:00]

> Best regards
>
> *Antony FORNES*
>
> Chargé d’Ingénierie documentaire
>
> Mission Services à la recherche
>
> Bibliothèques Université Côte d’Azur
>
> Parc Valrose, 06101 Nice Cedex 2
>
> */Tél :/*04 89 15 13 08
>
> https://bu.univ-cotedazur.fr <https://bu.univ-cotedazur.fr/>__
>
> 	
>
>
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-- 
Dr. Saulius Gražulis
Vilnius University Institute of Biotechnology, Saulėtekio al. 7
LT-10257 Vilnius, Lietuva (Lithuania)
fax: (+370-5)-2234367 / phone (office): (+370-5)-2234353
mobile: (+370-684)-49802, (+370-614)-36366

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