[Cod-bugs] PubChem link

[Robert McMeeking - STFC UKRI]

Dear Antanas

Thank you for getting back, and updating me on the situation. I just happened to spot this entry by chance. It just happened to be the latest update when I checked the COD site. Sadly I have no automatic checking procedure for this sort of thing!

Best Regards

Bob

From: Antanas Vaitkus <antanas.vaitkus90 at gmail.com>
Sent: 18 August 2025 21:47
To: McMeeking, Robert (STFC,DL,SC) <robert.mcmeeking at stfc.ac.uk>
Cc: cod-bugs at ibt.lt
Subject: Re: [Cod-bugs] PubChem link

Dear Robert,
Thank you for reporting this. We will address this the next time
we sync with PubChem by either updating or retracting the entry.

Unfortunately, there are very likely many more such errors as there are
too many entries to check by hand thus resorting to less precise automated
linking (see paper [1] for more details). We do run several automated data
quality checks to weed out the obviously incomplete structures, however, this
one seems to have slipped past our filters. Normally, we would expect the crystal
summary formula to include the missing H2O moieties, i.e. we expect it to
provide the idealised crystal formula, however, the original depositor might have
been following different conventions and simply calculated the formula only from
the resolved atoms.

We would be grateful if you could report any other such discrepancies you notice
in the COD x PubChem linkage.

Also, did you detect this error accidentally or were there any automated checks
involved? Maybe we could also include those in our workflow.

[1] https://jcheminf.biomedcentral.com/articles/10.1186/s13321-023-00780-2
Sincerely,
Antanas

On Mon, 18 Aug 2025 at 20:43, Robert McMeeking - STFC UKRI <robert.mcmeeking at stfc.ac.uk<mailto:robert.mcmeeking at stfc.ac.uk>> wrote:
Hi

I have noticed the recent additions of PubChem links – good work.

I happened to look at COD 1529982. This is the structure of KI(H2O)2, but the coordinates of the H2O moiety have not been located. This links is to the PubChem KI entry. The links both ways are a bit misleading!

Best Regards

Bob

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Antanas Vaitkus,
Vilnius University,
Life Sciences Center,
Institute of Biotechnology,
room C521, Saulėtekio al. 7,
LT-10257 Vilnius, Lithuania


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