[Cod-bugs] Questions about COD

[HERBET Marie-Emilia]

Dear Saulius,

Thank you very much for all the information provided and the accuracy of your answers.
On the license issue, I agree with you as researchers are supposed to cite properly other authors even if the CC-BY license is not specifically mentioned.
Thank you as well for clarifying the properties of COD-ID, which is a sort of ‘in-house’ permanent identifier as far as I understand, different from ARK or DOI but having the same function.
One of our criteria consists in checking the data quality management of repositories. In cristallography, it is common to have a two-step process: automated check of CIF files and manual check by experts. Can you confirm that COD still performs manual inspections as described in this paper:

https://academic.oup.com/nar/article/40/D1/D420/2903497

Last but not least, I would like to know why some researchers might decide/prefer to deposit their structures in COD rather than CSD as both services are free and cover the same disciplinary field. I don’t know if COD has already carried out a survey amongst its users but it would be great if you could elaborate a little bit on COD approach vs CSD, whose financial model is quite different.

Thank you again for your help and insight.
Best regards,
Marie


Marie-Emilia HERBET
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De : Saulius Gražulis <grazulis at ibt.lt>
Envoyé : mercredi 5 avril 2023 08:25
À : HERBET Marie-Emilia <marie-emilia.herbet at univ-lyon3.fr>
Cc : cod-bugs at lists.crystallography.net
Objet : Re: [Cod-bugs] Questions about COD

On 2023-04-04 11:35, HERBET Marie-Emilia wrote:
Thank you for all the information provided below. I get back to you with another question regarding COD. In the framework of our project aiming at building up a data repository selection tool for reasearchers, I would like to know if COD ID has the same features and role as a DOI. In other terms, does it act a permanent identifier that can be cited and accessed even if the URL changes?

Yes, indeed, the COD IDs are stable permanent IDs. Even when the data are no longer available (e.g. the structure is retracted), the ID stays and the metadata are further available. The COD IDs function as any other permanent IDs required to identify a data record, e.g. Archival Resource Keys (ARK), Handle identifiers, URNs; and, yes, DOIs are in the same category (except that you need to pay money to get DOIs assigned :/ ).

In addition to that, COD URLs (which are actually URIs) of the form 'https://www.crystallography.net/cod/2000000.html' or 'https://www.crystallography.net/cod/2000000.cif'are intended to remain stable into the future and can be used as COD structure identifiers.
Regarding my previous question related to licenses, the idea was not to promote copyright but rather to ensure that structures can be freely reused and cited using for instance CCBY license instead of depending on the license of the paper in which the structure is described (which often entails copyright rules applied by publishers.)

Well, this was discussed in the COD AB, and the current collegial decision is to put CC0 in the COD.

If you feel very strong about the issue, you can submit a "COD Improvement Proposal" to the COD AB (or to the cod-bugs@ list), and I'll forward it to the COD AB and promise to organise an on-line discussion (you would be welcome to participate in it).

We need to take into account that CC-BY is more restrictive for data users than CC0, so we need to look carefully as to not jeopardise their work flows. Most (all?) of our users, however, already now cite the original works since this is the custom in the academic community, so CC-BY might be not that disruptive after all.

Sincerely yours,
Saulius

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Dr. Saulius Gražulis

Vilnius University, Life Science Center, Institute of Biotechnology

Saulėtekio al. 7, LT-10257 Vilnius, Lietuva (Lithuania)

phone (office): (+370-5)-2234353, mobile: (+370-684)-49802, (+370-614)-36366

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