[Cod-bugs] Missing Journal Information

Thu Jul 3 14:00:57 EEST 2025

Hello Saulius

Thank you very much for the feedback. Getting my brain working again after being on a long holiday was a bit of a struggle! I am, however, now in a better position to streamline my processes at this and also.

I have checked a number of the entries on the COD site and they now look fine. I assume you are happy to map the Article ID onto the Start Page where this is appropriate. In the longer term perhaps “Article ID” might be a new field?

The CrystalWorks link:
https://cds.dl.ac.uk/cgi-bin/rfm/crystalworks_trawl_new?8799_8892_9714

does not pick up the amended details as yet, but I am assuming it will be become available after the next overnight upload to our server – if not tomorrow quite soon. I will get back if there are any issues to report.

Best Regards

Bob

From: Saulius Gražulis <grazulis at ibt.lt>
Sent: 03 July 2025 10:27
To: McMeeking, Robert (STFC,DL,SC) <robert.mcmeeking at stfc.ac.uk>; 'Antanas Vaitkus' <antanas.vaitkus90 at gmail.com>
Cc: 'cod-bugs at ibt.lt' <cod-bugs at ibt.lt>
Subject: Re: [Cod-bugs] Missing Journal Information

Dear Robert,

the records you mentioned in your file are updated, please have a look. I've checked several selectively, all looks right.

The TSV file is perfect, I would just add column names as the first line, as permitted in the RFC 4180 (i add an example of the same original TSV, supplemented by column headers).

The total work time for me to convert, update and check the COD from you file is about 1h, so this is a considerable saving from what I would have to do if I collect the data myself. Also, it does not depend much on the number of records to process (updating 200 records from the same table would take about the same, maybe checking lower percentage of update records than now). Thus I can squeeze this update into my schedule predictably. So this is a very significant help from you, thanks a lot once more!

If you have more of these please let us know :), I understand that it takes time to collect the data reliably, but all help from community is highly appreciated, we simple can not do all of it ourselves :)

Sincerely yours,
Saulius

On 2025-07-02 18:13, Robert McMeeking - STFC UKRI wrote:
Hello Saulius

I have been away on holiday and accessing the various files has been more of a problem than I anticipated. I am back now, but for various reasons may access is more restricted than I had hoped.

However, I have managed to generate a .tsv file, which I include as an attachment.

I downloaded the details from CrossRef searching on DOIs

The fields in the .tsv are:

  1.  COD Collection code
  2.  Article identifier
  3.  Journal Vol
  4.  Journal Issue
  5.  Start page no
  6.  End page no
  7.  Journal Title
IUCr has Article identified but no page numbers as far as I can see
Acta Cryst E has no article identifier
I have edited the full title for Acta Cryst E to correspond to what I believe you normally use.

I hope this is helpful!

Best Regards

Bob

From: Saulius Gražulis <grazulis at ibt.lt><mailto:grazulis at ibt.lt>
Sent: 19 June 2025 09:53
To: McMeeking, Robert (STFC,DL,SC) <robert.mcmeeking at stfc.ac.uk><mailto:robert.mcmeeking at stfc.ac.uk>; 'Antanas Vaitkus' <antanas.vaitkus90 at gmail.com><mailto:antanas.vaitkus90 at gmail.com>
Cc: 'cod-bugs at ibt.lt<mailto:cod-bugs at ibt.lt>' <cod-bugs at ibt.lt><mailto:cod-bugs at ibt.lt>
Subject: Re: [Cod-bugs] Missing Journal Information

On 2025-06-19 11:06, Robert McMeeking - STFC UKRI wrote:
I do appreciate that getting the full bibliography details is not the major COD priority, especially when a DOI link is available. But have you had any further thoughts on the entries linked to in my previous email?

I was thinking of making some more checks.

If you could convert that information to a .patch file (diff) against the existing COD CIF, we could then apply it and commit after the check. Is that a lot of work on your side? Alternatively, can you generate the information in some machine readable form (CSV or TSV preferred)?

Regards,
Saulius

--

Dr. Saulius Gražulis

Vilnius University Institute of Biotechnology, Saulėtekio al. 7

LT-10257 Vilnius, Lietuva (Lithuania)

mobile: (+370-684)-49802, (+370-614)-36366

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Dr. Saulius Gražulis

Vilnius University Institute of Biotechnology, Saulėtekio al. 7

LT-10257 Vilnius, Lietuva (Lithuania)

mobile: (+370-684)-49802, (+370-614)-36366

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