User talk:Egon Willighagen

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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)

CAS RN

Hi, I don't think that number of records you were adding belong to the WD property item. Regards, —mykhal (talk) 10:10, 3 March 2025 (UTC)

You prefer to have it on CAS Registry Number (Q102507)? I do not remember why I started those on the property and no objection to moving it. --Egon Willighagen (talk) 12:37, 3 March 2025 (UTC)

Moved. Egon Willighagen (talk) 12:59, 3 March 2025 (UTC)

Recreation of deleted item

I have deleted Q134351214 because it appears to be a recreation of deleted item Q134100253. This means that we have already made a decision that this entity does not satisfy our notability criteria. Please do not recreate deleted items, as they are likely to be deleted again immediately, and your account may be blocked.To appeal this decision, see Wikidata: Guide to requests for undeletion. Bovlb (talk) 21:06, 5 May 2025 (UTC)

Hi @Bovlb, thanks for letting me know. And noted. I did not intentionally recreate a deleted item. How did you find out? That seems to be a Wikidata skill that I lack. --Egon Willighagen (talk) 05:46, 6 May 2025 (UTC)

Yes, it's not as easy to find out as it should be. There is a tool, but currently it is only accessible to administrators and rollbackers. Bovlb (talk) 14:51, 6 May 2025 (UTC)

User talk:Wostr

Hi -> Wenn Du möchtest kannst Du mal auf Wostr Diskussionseite vorbeischauen. Da habe ich auch viele Frage gestellt. Leider hat er wenig Zeit um diese zu beantworten.
PS: Der Blue Obelisk wurde ja seit 2017 nicht mehr vergeben oder habe ich einfach die Infos nicht gefunden. Und bist Du der Meinung das in de-Artikel noch was rein muss? Calle Cool (talk) 22:30, 26 August 2025 (UTC)

I think we need a different way to discuss individual entries, I think. Not sure how yet. I will try to have a look at your questions asap.

About the Blue Obelisk Awards, yeah, I would like to see it return too. I have been exploring options but not managed to set up a award committee yet. My German is not good enough to understand your last sentence. Egon Willighagen (talk) 07:32, 27 August 2025 (UTC)

Q15478639

Hi - I have this SciFinder Information about CAS 114045-20-4. When I search with the IncKey in Wikidata, i get Q15478639. Now I now from Wostr that the SciFinder-IchlKey is not everytime right. So now my Qestion can I add 114045-20-4 to Q15478639 or have I to add a new item? Normaly CAS are for a defined structure and not a group... Calle Cool (talk) 10:01, 3 September 2025 (UTC)

hmm or the german Description with "Stofgruppe" is wrong...--Calle Cool (talk) 10:07, 3 September 2025 (UTC)

The CAS seems to me a match for Q15478639. -- Egon Willighagen (talk) 19:28, 7 September 2025 (UTC)

Q104999928

Can I add here CAS 34272-52-1? I doubt because in Pbuchem I get ID 6442677 for the CAS but PubChem-ID 21726728 you get with the IchlKey and is added in WD-Objekt Q104999928 Calle Cool (talk) 10:15, 3 September 2025 (UTC)

CAS 34272-52-1 and SMILES of Q104999928 are a match. The CAS number in PubChem seems wrong then. The PubChem CID in Wikidata matches the InChIKey in the same Wikidata item, as well as matches the InChIKey for the CAS number. -- Egon Willighagen (talk) 19:43, 7 September 2025 (UTC)

Q106902956 VS Q27257256

Same or somthing different? Both have the same CAS in... Calle Cool (talk) 14:53, 3 September 2025 (UTC)

hmm in Q27257256 we have the Information that it is a sub class from Q106902956.. Then the CAS in Q106902956 is wrong? And is in this case Q106902956 a group?--Calle Cool (talk) 14:55, 3 September 2025 (UTC)

Well, the CAS on Q106902956 is I think wrong. I had added that in 2022, so must have been part of the Common Chemistry data set I had access to at the time. There were errors in that file. Based on the current SciFinder, CAS 3376-24-7 should only be on Q27257256. I removed the CAS number from Q106902956.

@Calle Cool, thanks for this and the other reports! -- Egon Willighagen (talk) 19:47, 7 September 2025 (UTC)

Thanks for you Answers and correction. Pls note - I have add CAS 52392-70-8 to Q106902956 because Inchl is the same.--Calle Cool (talk) 10:16, 8 September 2025 (UTC)

I think that this discussion is resolved and can be archived. If you disagree, don't hesitate to replace this template with your comment. Calle Cool (talk) 14:55, 9 September 2025 (UTC)

Waixenicin A

Fürst Question: Q27089212 VS Q104401962 Could you add better names with Stereoinformation and have I add Chemspider and CAS to the right one? And then i find at Chemspider follow: ID 10311262, ID 16738585, ID 34981020 Which is now for wich WD-OBject? Calle Cool (talk) 10:37, 8 September 2025 (UTC)

Yeah, that's a complicated one. It seems the data in Wikidata is not consistent. Need to think about this one. Egon Willighagen (talk) 14:58, 15 September 2025 (UTC)

Waixenicin B

Q136159750 -> Wich is the right ChemSpider? IF I search with word "Waixenicin B" I get one Target. If I search with "Waixenicin-B" I get 11 tragets.. Calle Cool (talk) 10:42, 8 September 2025 (UTC)

Natural products are really hard. Even literature with structure elucidation is not always correct. Projects like LOTUS (Q104225190) are the one to look at for those. -- Egon Willighagen (talk) 15:03, 15 September 2025 (UTC)

Q126609793 4-Oxo-4-phenylmethoxybut-2-enoic acid

Hi - I find Pubchem 6437229 it has the same CAS as 106597 So the question -> have I to add 6437229 to Q126609793 too or need it a own Object? And is it right to add CAS 99058-77-2 to Q126609793 or need it a own Object? Calle Cool (talk) 11:41, 11 September 2025 (UTC)

CAS 99058-77-2 is definately not the same compound as Q126609793. When comparing Wikidata with PubChem, they must have the same InChI(-Key). If that is the case, then the match, if not, then the PubChem ID need to become a new Wikidata item. -- Egon Willighagen (talk) 15:02, 15 September 2025 (UTC)

Q136216178 Methylcopper

I have add two pubchem ID´s -> One I have find with CAS-Number and one which IchlKey -> are both right? Calle Cool (talk) 11:57, 11 September 2025 (UTC)

Anything with metal elements does not work well in neither Wikidata nor PubChem. We have to wait until the inorganic InChI comes out (can happen any day noe). -- Egon Willighagen (talk) 14:59, 15 September 2025 (UTC)

Q129393141

PubPeer’s secret is out: Founder of controversial website reveals himself (Q129393141) is an interesting item. Sensational title, but the DOI does not resolve, and all the matches in the Wayback Machine are error pages. Also, the published-in value doesn't really make sense. Is this the database equivalent of a copyright trap (Q1646902)? (While I do currently have a contract with PubPeer, this inquiry is not on their behalf; I discovered it incidentally.) Harej (talk) 23:05, 17 September 2025 (UTC)

@Harej, oh, fascinating! the article does not seem to be retracted in RetractionWatch/CrossRef, but clearly has been retracted. Looking at the item, I added this with, I guess, Scholia, and the data most certainly came from CrossRef. I have to come back on this. -- Egon Willighagen (talk) 05:15, 18 September 2025 (UTC)

@Harej, yeah, the DOI resolving is broken, but with a full text search in Google in the title I found it at a different URL, confirmed with the DOI on that page. So, it just seems to be broken DOI metadata: the page moved and Science forgot to update the metadata. I file a bug report with CrossRef, which will pick it up with the publisher (I think). -- Egon Willighagen (talk) 05:21, 18 September 2025 (UTC)

CrossRef took note and will pass on the information. They also suggest that people should contact the publisher. I wonder if we need a Wikibase to report DOI issues. -- Egon Willighagen (talk) 08:47, 19 September 2025 (UTC)

Benzomalvin A

Is Q77280044 a subclass of from Q82911675? Same qestion for Q105368960. And is Q77280044 = (-)-Benzomalvin A and Q105368960 = (+)-Benzomalvin A? Calle Cool (talk) 11:59, 23 September 2025 (UTC)

Hmm If I see CAS 157047-96-6 Q82911675 is (-) and not Q77280044... I have know changed it as I mean that is it right - Perhaps you can crosscheck it...--Calle Cool (talk) 15:40, 23 September 2025 (UTC)

I think Benzomalvin A (Q77280044) should indeed be subclass of (-)-Benzomalvin A (Q82911675) (which I think has incorrect names, as the names suggest a specific stereochemistry, which the structure does not have). The naming suggestion sounds reasonable, but not an expert in natural product naming conventions. I checked the CAS number, and the CAS record is inconsistent. The 2D drawing, SMILES, InChI, and InChIKey are for the stereoaspecific compound (ie. (-)-Benzomalvin A (Q82911675).

@AdrianoRutz, can you plz check too? Egon Willighagen (talk) 11:19, 27 September 2025 (UTC)

I think Benzomalvin D (Q136374171) and (-)-Benzomalvin A (Q82911675) are actually atropisomer (Q757764)s (see Interrogation of Benzomalvin Biosynthesis Using Fungal Artificial Chromosomes with Metabolomic Scoring (FAC-MS): Discovery of a Benzodiazepine Synthase Activity. (Q52658206)). I don't think I saw atropisomer (Q757764) pairs modeled on WD until know so it is still a challenge as they will be mixed in a lot of sources. The subclass of (P279) relationship seems correct but not the stereoisomer of (P3364) statement on (-)-Benzomalvin A (Q82911675), I think it should be on Benzomalvin A (Q77280044). (I think the name of (-)-Benzomalvin A (Q82911675) is wrong and should be something like "Benzomalvin A (undefined stereochemistry)", or similar. This should then solve the confusion AdrianoRutz (talk) 11:03, 28 September 2025 (UTC)

Mini Wikimedia Hackathon

Hoi, we organiseren weer een Mini Wikimedia Hackathon in Utrecht op 25 oktober. Misschien wat voor jouw? Het is kleinschalig, technisch georiënteerd en in-person. Als dit bij jou past kan je je aanmelden via de evenement pagina Daanvr (talk) 15:44, 6 October 2025 (UTC)

Hoi @Daanvr, bedankt voor de tip! De late reactie is vooral omdat ik het lang heb overwogen. Maar vrijdag ben ik in Groningen voor het Open Science Festival (en heb dan al twee dagen reizen achter de rug), en zaterdag ga ik mijn verjaardag vieren. Ik ga het moeten laten schieten :/ -- Egon Willighagen (talk) 10:16, 21 October 2025 (UTC)

Hoi @Daanvr, hoe was het geweest gisteren? -- Egon Willighagen (talk) 13:14, 26 October 2025 (UTC)

Hoi Egon\! Het was gezellig en productief, jammer dat je er niet bij kon zijn. Omdat je vorige keer interesse toonde maar het qua timing niet uitkwam, wil ik je wijzen op een groter evenement: de Wikimedia Hackathon Northwestern Europe 2026, op 13–14 maart in Arnhem. Het is een tweedaagse, technisch georiënteerde hackathon. Inschrijving sluit medio januari of zodra vol. Hopelijk past de timing dit keer beter\! Daanvr (talk) 23:56, 4 January 2026 (UTC)

Q136750539 and Q136749099

Hi - I have a problem with ChemSpider. First: All ditales for both WikidataItems are from SciFinder.
When you search at SciFinder with The CAS 2120392-49-4 (Q136749099) you find ChemSpider ID 73956592. But wehn you Look at Chemspider 73956592 saved InchIKey you get ORRSNYROBCDCFA-UHFFFAOYSA-N which is from CAS 2801565-54-6 (Q136750539).
First Question: In which Item is the ChemspiderID right?

Now I have find at chemspider ID 129767133] with Information CAS 2801565-54-6 (Q136750539), But the mention IchlI key at Chemspider is ZNLKFTSJPLUYPY-UHFFFAOYSA-O, waht is not 2801565-54-6 according to SciFinder.
Secound Questeion: If you were able to assign the first one, can that be added to the other Wikidata item, or would a different ChemspiderID be more appropriate?

PS: ZNLKFTSJPLUYPY-UHFFFAOYSA-O I haven't yet had it checked with SciFinder. Calle Cool (talk) 07:48, 10 November 2025 (UTC)

And if Helpfull In SciFinder you have also follow Information:
2801565-54-6 (Q136750539)
C43H51N4O3.Cl
Components: 2
Component RN:2120392-49-4 (Q136749099)--Calle Cool (talk) 07:57, 10 November 2025 (UTC)

PubChem 154723800

Hi - is PubChemID 154723800 in Q136702985 right (Same ichliKey) or in Q136750874 (Same CAS)? Calle Cool (talk) 09:31, 10 November 2025 (UTC)

PS: The maindatas from Q136702985 and Q136750874 are from SciFinder.--Calle Cool (talk) 09:34, 10 November 2025 (UTC)

Match with PubChem is always based on the InChI (-Key). That must match. PubChem has sufficient incorrect CAS numbers as those our provided by organisations uploading them, and since CAS is not open (except for Common Chemistry), they cannot routinely check correctness of CAS numbers. -- Egon Willighagen (talk) 18:36, 15 November 2025 (UTC)

Thanks for the explanation and the Updat from the WD-Objects – so I've actually been doing it wrong all along. In the past, I first searched for the CAS number on PubChem, and only if there was no match I look up the IchiKey. I'll do it differently from now on.

Regarding Common Chemistry: Who or what actually decides which CAS numbers are made public? Do you know?--Calle Cool (talk) 08:22, 17 November 2025 (UTC)

CAS does that. For the recent 500k release, they asked the community which compounds were important to them, and from this they derived the current list.

PS. we started writing up some curation approaches: https://blueobelisk.github.io/wikidata-chemistry-curation/ -- Egon Willighagen (talk) 08:34, 17 November 2025 (UTC)