Wikipedia talk:WikiProject Chemistry/CAS validation

message: *http://www.chemspider.com/blog/cas-discourages-using-scifinder-to-help-curate-wikipedia-structures-and-cas-numbers.html   --ChemSpiderMan (talk) 00:25, 11 March 2008 (UTC)
thread_title:  Blog Feedback 

message: I've looked at the first block, and there appear to be some problems with stereochemistry already. A few comments. To check the pdf against scifinder as-is (for someone using only one monitor/laptop screen) requires a lot of alt-tab window switching. Copying individual CAS numbers from the PDF into the Scifinder window (which can accept a text file or multiple lines) is not very efficient.
Tony, is there a way to generate the list in an excel file, CAS on left, structure on right, which I can print out? Then I can copy 10 or 25 CAS #s onto SciFinder, print out, and check one by one? It'll a lot of paper compared with printing the 25 pages as 25 pages. 
Walkerma, I'll send you a summary of the Scifinder output by email. --Rifleman 82 (talk) 09:30, 26 January 2008 (UTC)
replies: text: Yes, I can generate an Excel like file for you and send it forward. More work for me but it will reduce the work for you all so I'll do it. I'm not sure when I'll get to it but I might get it done today. If not today then it's unlikely to be until next week because of some meetings I am hosting next week.--ChemSpiderMan (talk) 13:44, 26 January 2008 (UTC)
replies: text: Rifleman...before I wade too deeply into the issues can you comment on the problems you are seeing? Lack of stereochemistry? Incorrect stereochemistry...I assume the latter. What we have to agree on is whether the primary key is the structure name and find the CAS reg number that matches that and adjust the structure to that. The problem is if the name itself is "too general". What we need to make sure of is that the CAS Number doesn't become the primary key and things are adjusted around that to far. These is much easier to explain in an interactive dialog if we can have one--ChemSpiderMan (talk) 15:43, 26 January 2008 (UTC)
thread_title: First block of 25

message: Rifleman...I have sent you and Walkerma the first 50 records in Excel format. I have now started re-checking those records based on your information. I can confirm there ARE issues with stereochemistry. The problem is where? Now that the structures and the IUPAC names on Wikipedia match the disconnect with the CAS number. So, is there a DIFFERENT CAS number for the structure drawn/...my expectation is YES...so you would need to draw the structure to do the search to get the correct CAS number OR the fact is the structure itself is wrong. How do we figure some of these out? This undertaking just got a whole lot bigger gentlemen...a lot bigger. We need to chat before it continues.--ChemSpiderMan (talk) 20:07, 26 January 2008 (UTC)
replies: text: Tuesday's not too far away. Can we do it then? --Rifleman 82 (talk) 02:50, 27 January 2008 (UTC)
replies: text: I will try and sit in on that discussion but have actually got someone visiting from Europe for the week and need to make the most of our time. I commit to attending the IRC chat provided I have internet access wherever I am at that time.--ChemSpiderMan (talk) 04:34, 27 January 2008 (UTC)
thread_title:  Stereo Issues on Structures 

message: Myself and Martin have compiled a list of some 2400 articles describing inorganic substances, which can be found at Wikipedia:WikiProject Chemicals/Inorganics. Most of these substances will have to be verified on the basis of a name, and many articles describe more than one substance. There are also substances which are described in more than one article. Any comments on the best way to proceed would be gratefully received! Physchim62 (talk) 14:56, 25 March 2008 (UTC)
thread_title:  Inorganics 

message: * Some background notes on . I am not a chemist; I do maintain Chembox.
# Drugbox. For this, it is best to also look at  (aka 'Drugbox'), and treat the same. In there, the identifiers mentioned here are equally present (eg Aspirin). Together, these infoboxes have  +  =  instances (infobox in article); almost all disjoint (not both infoboxes in one article).
# Read from WD. Today, three parameters are read from Wikidata, in both infoboxes (eg ammonia):
:::E number 
:::ECHA InfoCard ID 
::: (CompTox Chemicals Dashboard)
::The latter two can be locally overwritten (=overwrite WD value by entering a parameter value on enwiki; or 'none' to suppress).
::They have the option to Edit-At-Wikidata: the pencil icon that is a link to the Wikidata page (per good WP design: editors can edit!).
:: was added to Wikidata by :d:User:ChemConnector, to allow bulk-adding (April 2019). (Instead of: adding all values to enwiki infoboxes at enwiki, dewiki, ...). We could ask ChemConnector their experiences (working on Wikidata).
:3. IDs. As DMacks and Michael D. Turnbull noted here, the "1:1" relation between en-article and wd-QID ("ammonia" <-> "Q4087") is tricky. As far as I know, there has been no systematic check for correctness. For example, how is distinction of isomers, racemic, chiral compounds maintained? Wikidata people have build a orthography for this; I am not familiar with.
:In Chembox and Drugbox, variants are added by indexes: , , ..., ; and , ,  ..., . (eg Linalool, Dithiane). Apart from the soft guideline same-index-is-same-compound, no integrity checks are performed. See also .
:Chembox has no policy to handle InChI and Standard InChI systematically (both or one can be present).
:4. Validation. DMacks mentions the validation system, in use for both infoboxes (and not outside). It adds  or  to a set of parameters that have been verified (by a trusted editor). I have no guess on its completeness; it appears that many infoboxes have not been screened for this in a long time. For example,  has had between 1500 and 2000 articles 'forever'.
:-DePiep (talk) 13:35, 11 October 2020 (UTC)
thread_title: Chembox

message: :
::On validation, I have noticed many people have a template to use when they create a chembox that says that the entry is validated. So I suspect that the validation green ticks are not indicating that it has been checked by a "trusted user". If I find a red cross, yet the value appears correct, then I change it to the "correct" value. I assume this is how its supposed to work. But automated or semiautomated checks would be valuable. Because of "distrust" of wikidata, I would not recommend just applying the values found there. Instead we could have a hidden category that says there is a mismatch. For indexed chemboxes, perhaps qid(n) could be actually used or added to match up multi wikidata entries. I would also recommend that a list of mismatched entries should be made. This matching should also include German Wikipedia which also has good quality infoboxes. I suppose the Wikidata entries could also have a known good reference for the CASNo. Currently there are several references that are in use, but they are not all 100% good, and they all have missed entries. (eg PubChem, ECHA, ChemSpider) Graeme Bartlett (talk) 00:40, 12 October 2020 (UTC)
replies: text:  Quite possibly I've been doing the wrong thing but when I work on a chemical article at any length I always check all the Chembox lines that point to external databases and ensure that there is |StdInChI_Ref= or |ChemSpiderID_Ref= etc, then I delete the |Watchedfields = changed |verifiedrevid=464365162 lines (or set them to blank) so that the larger green/red ticks disappear from the bottom of the box. I assume that there is intended to be a bot that acts as guardian angel for certain values in a Chembox but absence of its |watchedfields flag is not an error. Michael D. Turnbull (talk) 11:37, 13 October 2020 (UTC)
replies: text: The validation in en:WP is done by CheMoBot by checking against a list of validated RevIDs.  The idea is that once validation is done on these stable fields, you don't (usually) need to change it.  For example, the CAS no. is very unlikely to change, so why should anyone ever need to edit that field?  (Yes - I accept that very occasionally there are revisions made - once in a blue moon.)  I did once see someone trying to vandalize the w:Sulfuric acid article ChemBox, and the bot caught it within about five minutes, adding the red X.  Walkerma (talk) 06:12, 14 October 2020 (UTC)
replies: text: That Bot last edited in June 2018. So it sounds inactive. But perhaps it could run again. Graeme Bartlett (talk) 02:27, 15 October 2020 (UTC)
thread_title: Chembox Validation, CheMoBot

message: ::Would it help if enwiki lists (catgegorises) all Chembox articles by CAS-comparision, like:
:::cat 1: WD enwiki: CAS same
:::cat 2: WD enwiki: CAS differ
:::cat 3: WD enwiki: one CAS missing
::: ...
:::cat X: Chembox with stereochemistry involved
::-DePiep (talk) 12:34, 5 April 2021 (UTC)
replies: text: Thinking: why not concentrate on  (with 6800 CAS RNs), instead of {Chembox} (11k)?  is by  already! -DePiep (talk) 19:20, 5 April 2021 (UTC)
replies: text:  I don't think that the difference between 11k and 18k (i.e. all compounds) is that great, if you can automate some of the checking so that human editors only have to reassess a small group of articles. While drugs are likely to have stereochemistry, the "common" CAS number will likely be the important one, that is, the one to have reached the market and have the significant body of publications. Simple compounds without isomer issues should only ever have had one CAS, I would hope, while inorganics will be a mess! There are, we know, examples like cyhalothrin with multiple marketed isomer groups. I can vouch that this one is already correct - but might be a good test of the automation ;-) Mike Turnbull (talk) 11:44, 6 April 2021 (UTC)
thread_title: Chembox support