From grazulis at ibt.lt Tue Apr 16 15:06:14 2024 From: grazulis at ibt.lt (=?UTF-8?Q?Saulius_Gra=c5=beulis?=) Date: Tue, 16 Apr 2024 15:06:14 +0300 Subject: [Cod-bugs] Information request for academic purposes In-Reply-To: References: Message-ID: <3651e4ed-e7a0-5415-cea4-860e11516fd3@ibt.lt> 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 Universit? C?te 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] Gra?ulis, 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* > > Charg? d?Ing?nierie documentaire > > Mission Services ? la recherche > > Biblioth?ques Universit? C?te d?Azur > > Parc Valrose, 06101 Nice Cedex 2 > > */T?l?:/*04 89 15 13 08 > > https://bu.univ-cotedazur.fr __ > > > > > -- > This message has been scanned for viruses and > dangerous content by *MailScanner* , and is > believed to be clean. > > _______________________________________________ > Cod-bugs mailing list > Cod-bugs at lists.crystallography.net > http://lists.crystallography.net/cgi-bin/mailman/listinfo/cod-bugs -- Dr. Saulius Gra?ulis Vilnius University Institute of Biotechnology, Saul?tekio al. 7 LT-10257 Vilnius, Lietuva (Lithuania) fax: (+370-5)-2234367 / phone (office): (+370-5)-2234353 mobile: (+370-684)-49802, (+370-614)-36366 -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.png Type: image/png Size: 11168 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: grazulis.vcf Type: text/vcard Size: 4 bytes Desc: not available URL: From grazulis at ibt.lt Thu Apr 18 09:34:52 2024 From: grazulis at ibt.lt (=?UTF-8?Q?Saulius_Gra=C5=BEulis?=) Date: Thu, 18 Apr 2024 09:34:52 +0300 Subject: [Cod-bugs] About the correct way to cite and reference COD data In-Reply-To: References: Message-ID: <92148173-0671-4931-a878-0defc1d6d789@ibt.lt> Dear Cristopher, thank you for inquiry and sorry for not answering sooner! I will give some recommendations regarding COD citation below: On 2024-04-09 05:15, CRISTOPHER ANTONIO MARTINS DE MOURA wrote: > I am a doctoral student in Ouro Preto, Brazil. > Initially, I would like to thank you for the ease of access to data. I > really like too much this database! > > I noticed that when using the data in my research, it is necessary to > reference the COD through 9 references, as shown in the link > https://wiki.crystallography.net/cod/citing/. > > I would like to know if I should also cite and reference the authors > of each data used. > > For example: > I am using the XRD pattern data of "COD ID 5000035" in my article. > Should I cite Will et al. (1988) and insert the bibliographic > reference in my article? > This is definitely a good move! You will give a credit to the authors who created the record. Another way to cite COD entry as a database record is suggested in our conference talks [1]. Briefly, you can either a) reference a CIF data stream (CID) or b) a "landing page" (HTML) and also either 1) reference a particular COD record revision that you have used or 2) reference a COD record, where the resolved ID (URL) will point at the newest curated revision of this record. Examples (from [1]): - for a 1a combination (please note the "@176759" at the end of the URL, which is the revision number): > Srivastava, R. C.; Klooster, W. T.; Koetzle, T. F. ?Neutron Structures > of Ammonium Fluoroberyllate? (1999) The Crystallography Open Database, > rev. 176759. The COD Advisory Board (eds.), > http://www.crystallography.net/cod/2002926.cif at 176759 [Retrieved > 2016-09-21 16:48 EEST] - for a 2b combination: > Srivastava, R. C.; Klooster, W. T.; Koetzle, T. F. ?Neutron Structures > of Ammonium Fluoroberyllate? (1999) The Crystallography Open Database. > The COD Advisory Board (eds.), > http://www.crystallography.net/cod/2002926.html [Retrieved 2016-09-21 > 16:48 EEST] Feel free to adjust this format to you journal's citation style (please regard the COD title as the title of a collective/periodic work and the COD AB as a collective editor of that work). Currently, the authors will most probably get more credit for their work if you cite the original publication, as you suggested. But the data citation "ecosystem" is changing, and I anticipate that the method suggested by me in [1] will become the mainstream one, especially when funding agencies and universities start recognising such citations as a part of your scientific output :). Of course you can add both citations ;) These methods are good when you are using just one or several entries from the COD and discuss them in more detail (or use them for the particular material identification). If you do statistics on a large number of COD entries (> 10), such method becomes impractical. In that case I suggest providing a list, in a CSV [2,3] or TSV [4] format, of the used COD entries and their revisions, and submit this file as a supplementary material for your paper. As a bare minimum, such file should contain COD IDs and COD revision numbers; if the space permits, it should contain the full bibliography of the original paper and the COD URL in addition to the COD ID information (as additional columns). HTH, Saulius Refs.: [1] Gra?ulis, 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] [2] Shafranovich, Y. (2005) Common format and MIME type for Comma-separated values (CSV) files. Series: Request for Comments, (4180), 1-8. IETF, RFC Editor. DOI: https://doi.org/10.17487/RFC4180 URL: https://www.rfc-editor.org/info/rfc4180 [3] Library of Congress (2021) CSV, Comma separated values (RFC 4180). 1-8. URL: https://www.loc.gov/preservation/digital/formats/fdd/fdd000323.shtml [accessed 2024-04-18T09:21+03:00] [4] Library of Congress (2021) TSV, TAB-separated values. 1-6. URL: https://www.loc.gov/preservation/digital/formats/fdd/fdd000533.shtml [accessed 2024-04-18T09:22+03:00] -- Dr. Saulius Gra?ulis Vilnius University Institute of Biotechnology, Saul?tekio al. 7 LT-10257 Vilnius, Lietuva (Lithuania) mobile: (+370-684)-49802, (+370-614)-36366 -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -------------- next part -------------- An HTML attachment was scrubbed... URL: