User talk:Egon Willighagen

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Hundreds of InChI duplicates

Hi Egon, please see the bottom 5-600 items of https://www.wikidata.org/wiki/Wikidata:Database_reports/Complex_constraint_violations/P235#Modified_unique_value_constraint

Probably you wanted to add missing ChEBI entries but didn't notice their SMILES containing asterisks. Please fix!

Thanks, SCIdude (talk) 17:31, 17 January 2023 (UTC)

Hi @SCIdude, thanks for the ping! I'll check what is going in. Egon Willighagen (talk) 17:55, 17 January 2023 (UTC)

Okay, the majority of the problems should now be fixed. I still don't understand what happened, because the code that I expect would have been used would ignore SMILES with a star. For the remaining items, I will see tomorrow what is left and fixed those manually. -- Egon Willighagen (talk) 19:47, 17 January 2023 (UTC)

Okay, cleaned up some last ones manually. BTW, it seems we also inherited some problems from ChEBI itself, see https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:64585 Here, the SMILES is not matching the depiction. Thanks again for spotting and highlighting this! I also have a nice curation step in mind: add CXSMILES for Wikidata entries without any SMILES and a ChEBI identifier (https://w.wiki/6EaE, well, this query is going to need some tweaking). Oh, and I used https://gist.github.com/egonw/01be540f50a620bddbe84f6cf86a8ac0 yesterday to find the problematic entries you spotted and prepare QuickStatements for removal of the problematic statements. -- Egon Willighagen (talk) 06:38, 18 January 2023 (UTC)

Thanks. In general I think these ChEBI entries are not very useful so better ignore them. SCIdude (talk) 09:30, 18 January 2023 (UTC)

Well, I cannot. We have a lot of them in WikiPathways but the same compounds actually also in LIPID MAPS. They are increasingly relevant. And we do have some time to work on these. -- Egon Willighagen (talk) 09:39, 18 January 2023 (UTC)

Question

Hello, is there any difference between Q56435819 and Q2377062? Karim185.3 (talk) 08:05, 8 August 2023 (UTC)

@Karim185.3: yes, they are different. The allylbenzene (Q56435819) is a specific chemical compounds, while phenylpropene (Q2377062) is a group of compounds (the French Wikipedia page lists a few of them). Egon Willighagen (talk) 08:08, 8 August 2023 (UTC)

Basic laboratory and industrial chemicals: A CRC quick reference handbook (Q22236188)

Is there any info about the pressure under which the boiling point was measured? [1] such statements give constraint violations ('pressure' qualifier is always mandatory for 'boiling point'). I suppose there is an indication somewhere that the pressure was 1013,25 hPa (given that other CRC handbooks usually uses this value as a 'standard' pressure for boiling points). Wostr (talk) 15:43, 11 August 2023 (UTC)

Yeah, unless otherwise specified, it's 101.325 kPa (same as the main CRC). I will add that. --Egon Willighagen (talk) 16:12, 11 August 2023 (UTC)

Updating in progress: https://chem-bla-ics.blogspot.com/2023/08/boiling-points-in-wikidata.html As a bonus, it adds pressure for some boiling points I added almost 5 years ago :) --Egon Willighagen (talk) 10:45, 12 August 2023 (UTC)

UreomiczBot

Hi Egon Willighagen, The last edits of your bot UreomiczBot date from November 19th, 2016. I would propose to remove its bot flag due to inactivity. Do you oppose to that? Lymantria (talk) 10:57, 8 November 2023 (UTC)

That is fine. In practice I like QuickStatements more because I can see better what is going on. --Egon Willighagen (talk) 12:52, 8 November 2023 (UTC)

Thank you. --Lymantria (talk) 13:52, 8 November 2023 (UTC)

MK-886 ./. MK-866

Hallo Egon! I have found a mixture of MK-886 ./. MK-866 in Q27086912. Could you create a new item MK-866 und split up all double properties? Thanks a lot. A commons category commons:Category:MK-866 is now avialable. Greetings JWBE (talk) 08:51, 28 December 2023 (UTC)

@JWBE, can you elaborate? I am not sure what you ask? I see the merger here: https://www.wikidata.org/w/index.php?title=Q27086912&diff=2038959051&oldid=1991860347&diffmode=source Please explain. Egon Willighagen (talk) 09:16, 28 December 2023 (UTC)

Maybe the merge had been accidently caused by me. It was not my intention. Could you split this up please? The splitted status is correct. MK-886 and MK-866 are different substances and have only a difference in a Butylgroup ./. a tert-Butylgroup. Thanks a lot. JWBE (talk) 18:14, 28 December 2023 (UTC)

Yes, I can do that. Egon Willighagen (talk) 18:29, 28 December 2023 (UTC)

@JWBE, okay, I had a go at it. Should be close to restored now. Egon Willighagen (talk) 18:36, 28 December 2023 (UTC)

Terglitol

I've started to modify Q1996360, Q63392135 and Q72426 but found out that many changes has been done by you not much earlier. Something seems wrong to me here, NP-40 (Q1996360) is not a class of compounds, but a specific compound and Nonoxynols (Q72426) is probably the correct class here? Wostr (talk) 12:55, 6 January 2024 (UTC)

I just another 10 or so, but the rest of the day I need to do other things. About NP-40 (Q1996360), the text was not entirely clear to me about this, but I gave priority to the diagrams in the EN and DE Wikipedias which say it is. But maybe more like a mixture? This needs further cleaning up and I did not get around to that. Something else, what are your ideas about all those organometallics? Shall we add SMILES for them too, or do we want to try something better/different? Egon Willighagen (talk) 13:05, 6 January 2024 (UTC)

Okay, I'll try to find some sources and clean this up. Regarding organometallics: SMILES is not a perfect notation not only for them but for many other classes of compounds, however, I have always believed that if we have even incorrect SMILES, but generated for a specific structure that cannot be represented better due to limitations of both the notation itself and the ability to represent chemical structures unambiguously, we should still include this type of notation in WD, possibly as deprecated with an appropriate qualifier. This is still a kind of chemical structure identifier, which may differ significantly from the actual structure, but which can still be useful, for example, when searching for specific chemical entities or comparing data between databases. Wostr (talk) 15:33, 9 January 2024 (UTC)

No rush. I will continue to work on it. Any curation we do here is new and we've been doing without for some items for years. Egon Willighagen (talk) 16:45, 9 January 2024 (UTC)