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Template-protected edit request on 2 April 2021

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I like to update the URLs to match the new CAS Common Chemistry database. Egon Willighagen (talk) 13:07, 2 April 2021 (UTC)

@Egon Willighagen:: {{Chembox CASNo/format/sandbox}} now has a copy of current code. You can edit & check it as you like. When OK, pls. reactivate the Edit Request (by setting |answered=no). Tests can be entered in /testcases2#CAS_number. -DePiep (talk) 15:11, 2 April 2021 (UTC)

I have used https://commonchemistry.cas.org/results?q= (for example ). (diff). Is that the right approach? -DePiep (talk) 15:53, 2 April 2021 (UTC)

More background: d:Wikidata_talk:WikiProject_Chemistry#Validation_of_CAS_numbers;_collaboration_with_Wikipedia? Wikidata. -DePiep (talk) 15:56, 2 April 2021 (UTC)

Using https://commonchemistry.cas.org/detail?cas_rn= (for example ). (diff). Is this the ANI? -DePiep (talk) 16:00, 2 April 2021 (UTC)

Yes, that looks right. --Egon Willighagen (talk) 19:04, 2 April 2021 (UTC)

Tests added to /testcases2#CAS_number. While some links might look slow or non-effective, the new URL is an improvement (which had more useless links, I'd say). Request reactivated. -DePiep (talk) 20:31, 2 April 2021 (UTC)

Request reactivated

Please replace all code from .../format/sandbox into live code: diff.

Change: using URL for new public CAS publication. -DePiep (talk) 20:31, 2 April 2021 (UTC)

To editors DePiep and Egon Willighagen:  done, and thank you both very much! P.I. Ellsworth  ed.  10:59, 3 April 2021 (UTC)

Unlinking commonchemistry based on Wikidata

I would like to complain about the last change inserted by Leyo on the 5 May 2021. It has resulted in unlinking many of the commonchemistry liks from chemboxes based on the vagaries of Wikidata. I used to rely on the link to verify if an entry was correct or not. But now with black unlinked entries it is harder to do. We have the CASNo_Ref to support a suitable reference for the CAS number if it has the cascite with CAS 2nd parameter then commonchemistry should get a link as that would then be valid. Otherwise perhaps we need a "CC" parameter instead of CAS if we want to limit to those entries verified in that database. You might say that Wikidata should be updated, but it isn't yet. I know how to add a CAS, but I do not know how to add any source in Wikidata.Graeme Bartlett (talk) 06:50, 6 May 2021 (UTC)

Are you sure that there are many missing links for compounds that have an entry in the Common Chemistry database? Egon Willighagen put a lot of effort to check and add references based on a spreadsheet he's obtained directly from CAS. It's actually not that difficult to add such a reference to Common Chemistry (see diff) manually.

The main target of Misplaced Pages articles are readers, not users. Hence, omitting broken links is of higher priority. Please note that if you bookmark https://commonchemistry.cas.org/detail?cas_rn=%s and follow these instructions you may quickly access the entry in the Common Chemistry database by e.g. simply typing cc into the address bar. --Leyo 12:13, 6 May 2021 (UTC)

More background. (it's complicated, as in: multiple rational influences interact). I've maintained {{Chembox}} many years; I am not a scientist nor a chemist. I do know about templates etc.

Main wiki actors are

enwiki: {{Chembox Identifiers}} (the infobox {{Chembox}} section showing CAS RN)

enwiki: |CASNo=

enwiki: User:CheMoBot the bot that handles {{Chembox}} changes (checking against earlier 'confirmed' values)

enwiki: {{cascite}}, the template that CheMoBot adds & edits, handling registered CAS NR edits; uses dedicated .._Ref= parameter: CasNo_Ref={cascite|changes|??} (iow, .._Ref does not contain a wiki-reference)

CheMoBot & {{cascite}} together create:

X CASNo_Ref={{cascite|changed|??}} → X

WD: QID carbon dioxide → carbon dioxide (Q1997)

WD: CAS Registry Number (P231)

-DePiep (talk) 20:04, 6 May 2021 (UTC)

May 7, late factual additions:

- enwiki {{Infobox drug}}: uses CAS RN too, presented in a ~similar way.

- enwiki numbers:

- {{Chembox}} : in 11461 articles

- {{Infobox drug}} : in 7378 articles

- sum: CAS RN in ~18k (mainsp) article infoboxes

May 7, end of late factual additions -DePiep (talk) 18:02, 7 May 2021 (UTC)

So. This needs a cleanup. DePiep

I advise

1. (let's) Drop the "verification" and CheMoBot process & statuses. No more or indicators any more. No reader understands those, and rightly so (because: Misplaced Pages does other routes of sources & trustIng)

It has created a *new* category of sourcing-editors, those who can declare an edit 'OK'. Also, it adds to the Reader page an extra, incomprehensible signal: the aye/nay hints. Even I do not know how to reach that "chemistry judging editor" status.

2. Then, go to a distinct true sourcing (aka ref) and External Link presentation (they are not the same).

3. Also, use WD at its best (and for 10k or 100k chemicals: we better use WD).

For now, I support Leyo's edit: "for CAS RN: when sourced in WD, do use WD".

-DePiep (talk) 20:30, 6 May 2021 (UTC)

If we are going to drop this chembox verification, or even talk about, we should do this in a more watched venue, say Misplaced Pages talk:WikiProject Chemicals. Graeme Bartlett (talk) 12:17, 7 May 2021 (UTC)

And when I say, many are missing, I mean on Misplaced Pages rather than wikidata. Wikidata seems to be more accurate. But we do get wrong pages linked or duplicate Wikidata entries. But that is not so much the issue here. I note a big effort in the last couple of days from Leyo‎; Project Osprey‎; and Michael D. Turnbull‎ to add CASNos Graeme Bartlett (talk) 12:25, 7 May 2021 (UTC)

I totally agree, User:Graeme Bartlett. Not just the validation ticks, but this whole discussion. OP User:Leyo, could you transpose this thread to WT:CHEMICALS? Maybe split topic talks are useful.

To be clear, GB, I had to mention this Validation process to describe the background. It was not my intention to stop the Validation (or start a descisive talk about that) via this obscure talkpage. Meanwhile, I do not have time enough now to set up such talks thoroughly (while such seriousness is needed). -DePiep (talk) 16:38, 7 May 2021 (UTC)

Wikidata CC sourcing module

MisterSynergy has developped a module that checks for a given CASRN if there is a reference to CAS Common Chemistry for this CASRN in the Wikidata item associated with the article. Please note that there are currently 128,980 Wikidata items] with such a reference (all recently added).
Hence, the code

{{#if: {{wd|property|sourced| |P231}} | <span title="commonchemistry.cas.org"></span> | {{{localValue}}} }}

might be replaced by

{{#if: {{#invoke:Sandbox/Leyo/CommonChemistry|entry_CAS_Common_Chemistry|cas={{{localValue}}}}} | <span title="commonchemistry.cas.org"></span> | {{{localValue}}} }}

The code will need to be adapted based on the final location of the Module:Sandbox/Leyo/CommonChemistry. --Leyo 09:40, 10 May 2021 (UTC)

If nobody objects, I would like to perform a live test. As it uses the Wikidata items associated with the articles, it is not possible to do a sandbox test. However, I did some test using the preview function. --Leyo 07:59, 11 May 2021 (UTC)

Does Wikidata allow sandboxes in Wikidata? Graeme Bartlett (talk) 11:02, 11 May 2021 (UTC)

I don't know, but I don't consider a representative test feasible, at least without a large effort (creating several pairs of article+item for different cases). On the other hand, the only thing that could probably happen in a life test is that links to Common Chemistry could be there, where they shouldn't and vice versa (which is not really a huge issue IMHO). However, do you have any special (in any kind) articles in mind where a test using the preview function could be interesting? --Leyo 11:34, 11 May 2021 (UTC)

@Leyo:, you could first try the basic situations by single previews, to visually check for unexpected results (or save-and-speedy-revert). After such cerefulness, no objection (and be prepared to revert).

BTW, no tracking category/ies projected? -DePiep (talk) 06:08, 12 May 2021 (UTC)

(more feature thoughts:)

Could the substance QID be added (optionally), e.g. for indexed substances (|CASNo1 ... CASNo5= can exist)). Also, the article's QID might not exactly represent the substance intended.

Some other {{Chembox}} parameters have the option |...=none, which would suppress any output. (overruling the WD then).

-DePiep (talk) 06:13, 12 May 2021 (UTC)

I am fine with tracking categories. What about Category:Chemical articles with CAS registry number in Common Chemistry database and Category:Chemical articles with CAS registry number not in Common Chemistry database, respectively? A shorter alternative could be Category:Chembox CAS registry number linked and Category:Chembox CAS registry number not linked.

The other ideas are worth considering at a later stage. I don't think we need to include them in the live test now. --Leyo 14:48, 12 May 2021 (UTC)

Maybe very short names, like Category:CAS RN from Wikidata (ie, no interpretation of the WD situation), Category:CAS RN .... -DePiep (talk) 15:18, 12 May 2021 (UTC)

Well, the CAS RN are not from Wikidata, just the switch whether a link to Common Chemistry is provided. --Leyo 15:30, 12 May 2021 (UTC)

see below #Setup Question -DePiep (talk) 16:43, 12 May 2021 (UTC)

About allowing setting the substance-QID: (a) useful when the articletitle/substance descr is not specific enough (racemic? generic? the major L-stereo?), and WD/CCdb is that specific (a major goal IIRC); also useful for testing off-article. And (b) QID input is required when using indexes (Category:Chemical articles with multiple compound IDs (2,231)); when the module is applied to every CAS RN/compound in the infobox.

-DePiep (talk) 15:18, 12 May 2021 (UTC)

Setup Question

Took a better look at your/MisterSynergy CC-module (great ambition!). I understand function "check_claim" checks whether the localvalue (|CASNo= input in the enwiki article) equals the CAS Registry Number (P231) value in WD for the same QID (+ other checks). If so, it adds the CC source (reference/link). IF OK, returns "1" -> show the source-reference.

? My question is: why involve checking the localvalue at all? Why not the routine: "if the QID has the CC-sourced value, show that value and ignore the localvalue". (And add to tracking eg "Category:CAS RN from WD" -- implicit also: CAS RN is sourced in CC).

This increases the number of CC-sourced CAS RNs (becasuse: wrong localvalue does not matter).

Failures (situation 'This Compound/QID is not CC-sourced in WD') are tracked in eg "Category:CAS RN not CC-sourced in WD" for maintenance! (This one needs attention, can help WD/CC, and shold be empty in the future :-) ).

localvalue (enwiki CASNo input) is only used when the module's WD-check fails and so is shown without any WD/CC data. The module can/should do the WD-data formatting too IMO, and the categorisation.

In short: "When WD-QID has CC-sourced CAS RN, show that one + link. If not, show localvalue + local fomatting".

It prevents mixing enwiki and WD data, and *having* to edit enwiki while the right CAS RN is in WD

(again, both for testing and CASNo-indexes it would be useful if the module uses an optional QID input).

All the best, -DePiep (talk) 16:43, 12 May 2021 (UTC)

I don't think that overwriting the local CAS RN with the one in the WD item would be accepted. But this may be discussed. For now, I started the live test. Please report any issues you might discover. --Leyo 19:34, 12 May 2021 (UTC)

"I don't think ... would be accepted" points to the core issue. I say we (=the whole enwiki/Wikidata Chemicals editorship) should strive for a cleancut solution: when well-sourced in WD, accept & use source in enwiki. Sure this takes a tough talk. -DePiep (talk) 21:04, 14 May 2021 (UTC)

Outcome

The live test revealed that the principle works. So far, I have not discovered any dead link in Category:Chembox CAS registry number linked. On the other hand, there are quite some article in Category:Chembox CAS registry number not linked that should not be there, i.e. their CAS RN should be linked. The reason for that is that the reference to Common Chemistry in the associated Wikidata has not yet been added. @Egon Willighagen: Could you have a look at the articles in that category and add the missing reference to the appropriate ones? --Leyo 20:31, 12 May 2021 (UTC)

What about excluding pages outside the article namespace from the tracking categories?

Articles with multiple CAS registry numbers are in Category:Chembox CAS registry number not linked, since only one CAS RN may be in the Wikidata item and thus linked. --Leyo 23:17, 15 May 2021 (UTC)

Problem with nonexistent Wikidata item

Hantzsch ester is in the hidden Category:Pages with script errors due to Module:Sandbox/Leyo/CommonChemistry asking for a non-existent Wikidata item in the following code (which calls {{Chembox CASNo/format}}):

{{Chembox Identifiers
| CASNo = 1149-23-1
| PubChem = 70849
| SMILES = }}

Presumably a fix would be for a Wikidata item for the article to be created but the module should do something more clever if there is no item. Johnuniq (talk) 03:21, 13 May 2021 (UTC)

It be easily fixable. Before possibly undoing my latest change, please save the list of articles in the tracking category „not linked“ (or in both). I am currently connected with my mobile phone and can’t do it myself. —Leyo 07:21, 13 May 2021 (UTC)

Category:Chembox CAS registry number linked has 7,853 pages and Category:Chembox CAS registry number not linked has 4,424 so I haven't bothered to save them. Evernic acid was just created and it has the same problem. There is no great urgency so please have a look when possible. Johnuniq (talk) 07:33, 13 May 2021 (UTC)

I had a quick look at the module and couldn't resist a couple of tweaks, one of which avoids the problem of a non-existent Wikidata item. Johnuniq (talk) 07:47, 13 May 2021 (UTC)

Great work, all! Just to get clear what is happening here... when you say "nonexisting Wikidata item", do you mean the (English) Misplaced Pages page does not have an associated Wikidata page at all, or is it just not connected via a sitelink? --Egon Willighagen (talk) 08:52, 13 May 2021 (UTC)

I wouldn't think there was an effective difference between an article with no Wikidata item and one which merely had not been linked to its item. It's not having a link which caused the problem which occurred on Hantzsch ester + Evernic acid + Merochlorophaeic acid if anyone wants to investigate (the last two are new articles). Johnuniq (talk) 09:16, 13 May 2021 (UTC)

I don't link these articles to WD for now to have them available as test cases. As Johnuniq has eliminated the script errors by improving the module, there is no hurry.

@Egon Willighagen: It would be great if you could check the CAS numbers of the articles in Category:Chembox CAS registry number not linked. It seems that for quite some there is an entry in the CAS Common Chemistry database, but the respective reference in the Wikidata items has not yet been added. --Leyo 22:34, 13 May 2021 (UTC)

Of the three specific items listed, I noted the second and third were linked yesterday. I linked the first one. So, these three are covered. In the full list, use this with care. I was just looking at Acetate which has a chembox, but that chembox is just an example, and it not expected to link to a Wikidata item. This happens a lot, when a class of compounds (like here), has one or more examples from the class. I have not idea yet how we want to solve this. For this, we would have the Misplaced Pages link with a sitelink to the Wikidata for the class of compound (like here: https://www.wikidata.org/Q212527) and each ChemBox to a Wikidata item separately. What if the ChemBox had an optional Wikidata field for such cases? --Egon Willighagen (talk) 15:17, 14 May 2021 (UTC)

Other compound classes with one or more ChemBoxes with one or more chemicals: Acetone peroxide, Acemannan --Egon Willighagen (talk) 18:26, 14 May 2021 (UTC)

I would propose to skip with special cases for now. --Leyo 21:23, 14 May 2021 (UTC)

Can you please have a look at a page like AEBSF? As far as I can see, it's been linked to Wikidata for some time now. Not sure why this is suggested as not linked. There are more of such what sound to me like false positives. --Egon Willighagen (talk) 18:45, 14 May 2021 (UTC)

All articles with a chembox (not a drugbox) in Category:Chemical articles with multiple CAS registry numbers contain this tracking category. Obviously, only one CAS RN is contained in the Wikidata item. All the others are currently not linked. --Leyo 21:23, 14 May 2021 (UTC)

So this is another challenge to add support for indexed entries with more than one CASNo. We could add another QIDx parameter to link to appropriate Wikidata items from the chembox. THere are situations where this would be useful. Graeme Bartlett (talk) 06:18, 16 May 2021 (UTC)

Another typical curation example is Anethole which may be the enantiopure form, but is currently not linked to the enantiopure form in Wikidata. Worse, it's also linked to the German Misplaced Pages which reflects a mixture. I am not currently sure what the English Misplaced Pages is supposed to link to in Wikidata, Q27105777 or Q255564. (This is also quite common situation in the Wikidata/Wikipedia linking.) BTW, Scholia's chemical "aspect" shows isotope and stereo variants, and can be helpful: https://scholia.toolforge.org/chemical-class/Q27105777 --Egon Willighagen (talk) 20:04, 14 May 2021 (UTC)

Yes, such cases cannot be easily solved. However, as there still are easy cases. Until this week, even articles of common chemicals such as Aniline, Acetylene or Acetone did not have a reference to Common Chemistry in the associated Wikidata item. These are cases to start with. --Leyo 21:23, 14 May 2021 (UTC)

That sounds easier than it is, actually. The CAS RN for Acetone is not validated because the input I got from CAS actually contains multiple records with the same InChIKey. So, algorithmically, it's not easy to recognize which CAS number is the correct one. --Egon Willighagen (talk) 21:32, 14 May 2021 (UTC)

Okay, I see. I had also checked https://commonchemistry.cas.org/results?q=acetone, where there is one hit only. --Leyo 22:37, 14 May 2021 (UTC)

Here's an example of where the info in the ChemBox is not consistent: Bactoprenol#Inconsistent_CAS_RN --Egon Willighagen (talk) 20:53, 14 May 2021 (UTC)

Resolved by Boghog. --Leyo 23:10, 15 May 2021 (UTC)

Validity check

In de.wikipedia, the validity of the check digit is analysed using the following code:

{{#ifeq: {{#expr: (
{{#expr:{{Str index|{{Str rightc| 000000000{{#if:Str trim|{{{1}}}}} | 12 }} | 1}}*9}} + 
{{#expr:{{Str index|{{Str rightc| 000000000{{#if:Str trim|{{{1}}}}} | 12 }} | 2}}*8}} + 
{{#expr:{{Str index|{{Str rightc| 000000000{{#if:Str trim|{{{1}}}}} | 12 }} | 3}}*7}} + 
{{#expr:{{Str index|{{Str rightc| 000000000{{#if:Str trim|{{{1}}}}} | 12 }} | 4}}*6}} + 
{{#expr:{{Str index|{{Str rightc| 000000000{{#if:Str trim|{{{1}}}}} | 12 }} | 5}}*5}} + 
{{#expr:{{Str index|{{Str rightc| 000000000{{#if:Str trim|{{{1}}}}} | 12 }} | 6}}*4}} + 
{{#expr:{{Str index|{{Str rightc| 000000000{{#if:Str trim|{{{1}}}}} | 12 }} | 7}}*3}} + 
{{#expr:{{Str index|{{Str rightc| 000000000{{#if:Str trim|{{{1}}}}} | 12 }} | 9}}*2}} + 
{{#expr:{{Str index|{{Str rightc| 000000000{{#if:Str trim|{{{1}}}}} | 12 }} | 10}}*1}} ) mod 10 }} |
{{Str index|{{Str rightc| 000000000{{#if:Str trim|{{{1}}}}} | 12 }} | 12}} |<!--ok-->| <span style="color:red">''' CAS-Nummer formal falsch''' </span> {{#ifeq: {{NAMESPACENUMBER}} | 0 | ] }} }}

What about introducing something similar here, too? --Leyo 14:28, 21 May 2021 (UTC)

• Calculation can be made more efficient using Module:String. BTW and interestingly, Wikidata can perform such number checks way more easily.

More important: I see no advantage checking enwiki CAS RN input. There is no use in having a categorising pages as "CAS RN incorrect number" -- because: what to do next? Also, CC is doing that for us, and we should put our effort in getting this right in Wikidata. Enwiki (like {{Chembox}}, {{Drugbox}}) then can easily use that cured and sourced data. Note that our 18k checmical infoboxes still have no check on accuracy or correctness (for example in chemical groups of stereochecmistry). There is no use keeping dabbling in enwiki pages.

-DePiep (talk) 11:59, 22 May 2021 (UTC)

If you can provide the code, I certainly wouldn't oppose using Module:String.

I do strongly disagree concerning your statement on categorisation. If a CAS RN is found to be incorrect, then it needs to be replaced by the correct one.

It's a fact that we currently use the CAS RN from the local articles, not from Wikidata. Hence, this is the basis for discussion. --Leyo 19:15, 22 May 2021 (UTC)

Yes bad CAS RN must be replaced. But this numbercheck is least relevant (sort of typo checking while the substance-definition question is the elephant). Better: compare enwiki local input with WD value, categorise when different. There is our curing job. We have no obligation to the {{cascite}} claims, it just might help a bit researching articles that are categorised. (technically, we could use the add-QID option to allow us to be more specific; eg versus article title).

More generic: shall we formally propose (RfC?) to change/define the CAS RN presentation? For example, we need to decide whether, in the infobox, we provide the source link (a ref then), of the External Link (EL) to the database. Of course I am thinking about the CC link. Also, I'd like to question the {{cascite}} 'validation' system -- which can be treated quite independently, to simplify the discussion. -DePiep (talk) 19:48, 22 May 2021 (UTC)

Template-protected edit request on 25 January 2022

This edit request has been answered. Set the |answered= or |ans= parameter to no to reactivate your request.

Please revert these edits last two from 5, 12 May 2021 (by Leyo).

Change: CAS RN link is not working any more. Worse: it introduced a /sandbox page in the live infobox (???).

Live check after this change: in Anethole, infobox Chembox "CAS Registry Number": 4180-23-8, should link to this simple url.

Good Report by Walkerma. DePiep (talk) 06:38, 25 January 2022 (UTC)

 Done. --Dirk Beetstra 07:59, 25 January 2022 (UTC)