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This is an old revision of this page, as edited by Andrew Su (talk | contribs) at 19:21, 26 January 2017 (→Comment on wikidata transclusion from the User:ProteinBoxBot team: r). The present address (URL) is a permanent link to this revision, which may differ significantly from the current revision.

WikiProject iconChemicals NA‑class
WikiProject iconThis page is within the scope of WikiProject Chemicals, a daughter project of WikiProject Chemistry, which aims to improve Wikipedia's coverage of chemicals. To participate, help improve this page or visit the project page for details on the project.ChemicalsWikipedia:WikiProject ChemicalsTemplate:WikiProject Chemicalschemicals articles
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WPChem worklist pages by quality
Quality
Total
FA 2
GA 16
B 172
C 76
Start 110
Stub 14
List 1
NA 4
Assessed 395
Total 395
WikiWork factors (?) ω = 1,486 Ω = 3.81

The worklist shows the actual work to be done to achieve the goals of the Chemicals wikiproject. The choice of important compounds articles to work on has been finalized in an earlier stage of the wikiproject (around mid 2005), and no further articles are added, although we remain open for strong suggestions on this talkpage. The work these days focuses on improving the articles, from Chem Stub all the way to Chem A-Class articles. The table below shows that progress.

Worklist historical status
2005 2006 2007 2008 2009
 
Grade 		Jun Oct May Oct Mar Oct Feb Aug Apr Dec
Template:Chem A-Class 29 26 32 32 33 25 25 23 18 18
Template:Chem B-Class 71 84 101 130 148 156 158 180 185 188
Template:Chem Start 112 131 199 190 174 174 180 153 160 161
Template:Chem Stub 97 130 46 29 27 27 19 26 19 18
unclassified 76 - - - - - - - - -
Total 385 371 378 381 382 382 382 382 382 382
percentage
≥Chem Start 		55.1 65.0 87.8 92.3 92.9 92.9 95.0 94.0 95.0 95.3
weighted
progress, % 		42.2 50.4 57.8 60.8 62.2 61.7 62.4 63.1 63.2 63.9


The percentage ≥ Chem Start was indicative of the initial effort. Now that we are progressing to more advanced progress, the weighted progress indicator is used, calculated as (Unclass*0 + Stub*1 + Start*2 + B-Class*3 + A-Class*4) / (Articles*4).


Chemicals articles by quality and importance
Quality Importance
Top High Mid Low NA ??? Total
FA 1 2 2 2 7
FL 1 1
GA 1 12 21 12 46
B 21 138 326 275 12 772
C 7 74 364 1,173 26 1,644
Start 96 1,140 5,284 133 6,653
Stub 340 10,337 2 146 10,825
List 2 7 1,551 50 266 1,876
Disambig 3 30 33
Template 383 383
NA 16 170 3,540 3,726
Other 1 19 20
Assessed 30 324 2,216 18,809 4,024 583 25,986
Unassessed 1 17 207 225
Total 30 324 2,216 18,810 4,041 790 26,211
WikiWork factors (?) ω = 107,199 Ω = 5.37


For the statistics for all chemicals, as registered by the bot, also see complete list

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  • 04 Nov 2024 – XW10508 (talk · edit · hist) AfDed by Toadspike (t · c) was closed as keep by Toadspike (t · c) on 06 Nov 2024; see discussion (3 participants)

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Molecule or salt ?

Which is the most correct structure for SeSn ? A covalent bond or a ionic bond ? See the table

Database Covalent Ionic
Wikidata Q6589976 Q27283356
PubChem 6432049 9877645
ChemSpider [www.chemspider.com/Chemical-Structure.4937309.html 4937309] [www.chemspider.com/Chemical-Structure.8053322.html 8053322]
InChI 1S/Se.Sn 1S/Se.Sn/q-2;+2
InChIKey MFIWAIVSOUGHLI-UHFFFAOYSA-N LYZMBUYUNBCSMW-UHFFFAOYSA-N

Snipre (talk) 15:45, 8 December 2016 (UTC)[reply]

The pictures drawn by these sites are nonsense. Get over it or get used to it. There is a reason that inorganic chemistry is distinguished from organic - and your questions illustrate one aspect of the difference - the structural chemistry in inorganic is a whole new game compared to the world of most organic compounds, which mainly conforms to well defined (computer-definable) structural rules and is mainly comprised of molecular species with low lattice energies that retain their structures in the solid and in solution. Not to say that one area is more advanced or better than the other (or even completely distinct as illustrated by organometallic chemistry). --Smokefoot (talk) 17:52, 8 December 2016 (UTC)[reply]
The structure would be a three dimensional lattice. Normally you would illustrate this with a diagram of the unit cell, and give the lattice parameters so you can tell how it fills space. Graeme Bartlett (talk) 21:41, 8 December 2016 (UTC)[reply]

2-Isopropyl-5-methyl-1-(2,6-dihydroxy-4-nonylphenyl)cyclohex-1-ene

Does this compound have a CAS RN? --Leyo 01:13, 7 January 2017 (UTC)[reply]

Not that I can find. Doing a similarity search gave an isomer with Me's added to alpha and beta carbons of the tail, and two fewer carbons in length. It has a paper and a patent, referring to cannabinoids. The propyl-tailed derivative gets 130 hits, again cannabinoid literature.--Smokefoot (talk) 01:25, 7 January 2017 (UTC)[reply]
Thanks. Did you do the search using SciFinder? --Leyo 20:01, 7 January 2017 (UTC)[reply]
I checked SciFinder; no exact hits, and the one Smokefoot notes--an isomeric nonyl sidechain--is the closest by similarity to it. No library near me has a copy of The Total Synthesis of Natural Products. (cited ref 1). I won't have access to the TetLett article (by the same author, cited ref 2) until Monday to see what it says, but I did a SciFinder search for all compounds in that article. It found several structures having that same isononyl sidechain but no other major alkyl-sidechain analog. I wonder if someone somewhere dropped a leading "isomer of" or "iso" on the "nonyl" name? DMacks (talk) 20:39, 7 January 2017 (UTC)[reply]
Meodipt created that article and should thus be in the position to answer that question. --Leyo 19:28, 17 January 2017 (UTC)[reply]
I will check in my copy of that article from Total Synthesis of Natural Products to confirm when I get a chance but pretty sure that structure matches what is in there. However it could well be a mistake in the review article, as dimethylheptyl would make more sense than n-nonyl in terms of substituents here. Don't think I ever double checked it against the original Tetrahedron Letters paper as I didn't have access either. Meodipt (talk) 02:11, 20 January 2017 (UTC)[reply]
BTW: This unsourced addition of a CAS RN by a new user might be checked. --Leyo 20:25, 7 January 2017 (UTC)[reply]
Structure found by SciFinder for that CAS looks like the same. DMacks (talk) 20:41, 7 January 2017 (UTC)[reply]
Thanks. --Leyo 23:58, 10 January 2017 (UTC)[reply]

Missing lower case redirects

For some reason, en.wikipedia prefers article names of chemicals to be in upper case, e.g. 1,1-Dibromoethane (not 1,1-dibromoethane). As in this example, the lower case name, i.e. how the name would appear in the text, is a red link. There are many more such red links that need to become redirects, e.g. these and those (some are false-positives). Is there an easy way to create the missing redirects? --Leyo 15:32, 10 January 2017 (UTC)[reply]

It might be an interesting feature-request to make the following expansion of long-standing wikilink handling: "treat first alphabetic character as capital even if other non-alphabetic characters are before it". Currently [[foo]] is treated as [[Foo|foo]], so this would extend the magic to [[1foo]] being [[1Foo|1foo]]. Take it to VPT (do they have a perennial-proposals archive)? DMacks (talk) 17:03, 10 January 2017 (UTC)[reply]
My intention was that the missing redirects are being created to eliminate red links. The feature request is probably a good idea, but may take way to long to get implemented (if at all). --Leyo 23:30, 10 January 2017 (UTC)[reply]

Inconsistency in article names of dyes

There are dye article names in upper case such as these

and in lower case such as those

Shouldn't we have a consistency in the naming? Please have a look at Category:Azo dyes and other articles in (subcategories of) Category:Dyes. --Leyo 15:11, 17 January 2017 (UTC)[reply]

I guess that the upper case spellings should be used since these are proper names.
Dyes and pigments are a problem in Wikipedia, at least for those that are not used in biomedical area. Unlike what most of us edit, they are actually used for something in the real world. Few editors have knowledge or interests in this area. One start would be to construct a work list of the most pervasive dyes and pigments. --Smokefoot (talk) 18:27, 17 January 2017 (UTC)[reply]
Well, there are List of dyes and List of inorganic pigments. --Leyo 19:25, 17 January 2017 (UTC)[reply]

WikiJournal of Medicine promotion

The WikiJournal of Medicine is a free, peer reviewed academic journal which aims to provide a new mechanism for ensuring the accuracy of Wikipedia's biomedical content. We started it as a way of bridging the Wikipedia-academia gap.[1] It is also part of a WikiJournal User Group with other WikiJournals under development.[2] The journal is still starting out and not yet well known, so we are advertising ourselves to WikiProjects that might be interested.

Engaging Wikipedians

  • Original articles on topics that don't yet have a Wikipedia page, or only a stub/start
  • Wikipedia articles that you are willing to see through external peer review (either solo or as in a group, process analogous to GA / FA review)
  • Image articles, based around an important medical image or summary diagram

Engaging non-Wikipedians

We hope that an academic journal format may also encourage non-Wikipedians to contribute who would otherwise not. Therefore, please consider:

  • Printing off the advertisement poster and distribute in tearooms & noticeboards at your place of work
  • Emailing around the pdf through contact networks or mailing lists (suggested wording)

If you want to know more, we recently published an editorial describing how the journal developed.[3] Alternatively, check out the journal's About or Discussion pages.

  1. ^ Masukume, G; Kipersztok, L; Das, D; Shafee, T; Laurent, M; Heilman, J (November 2016). "Medical journals and Wikipedia: a global health matter". The Lancet Global Health. 4 (11): e791. doi:10.1016/S2214-109X(16)30254-6. PMID 27765289.
  2. ^ "Wikiversity Journal: A new user group". The Signpost. 2016-06-15.
  3. ^ Shafee, T; Das, D; Masukume, G; Häggström, M (2017). "WikiJournal of Medicine, the first Wikipedia-integrated academic journal". WikiJournal of Medicine. 4. doi:10.15347/wjm/2017.001.

Additionally, the WikiJournal of Science is just starting up under a similar model and looking for contributors. Firstly it is seeking editors to guide submissions through external academic peer review and format accepted articles. It is also encouraging submission of articles in the same format as Wiki.J.Med. If you're interested, please come and discuss the project on the journal's talk page, or the general discussion page for the WikiJournal User group.
T.Shafee(Evo&Evo)talk 10:33, 19 January 2017 (UTC)[reply]

Comment on wikidata transclusion from the User:ProteinBoxBot team

I've copied my reply to this discussion at WP:MED because I think it's relevant here, and hopefully will prevent confusion or misunderstanding down the road...

Hello folks, speaking for the ProteinBoxBot team here. Let me provide a bit of context and history. Since ~2007, our team has been keeping the infoboxes on pages for human genes/proteins up to date. For many years, we have been making those edits using our User:ProteinBoxBot account. Our bot synced data from many source databases, and populated infoboxes here on Wikipedia using {{GNF Protein box}}. When Wikidata transclusion became possible, we made plans to convert our bot so that gene/protein data would be written to wikidata, and the relevant content would be queried from there. This was not a trivial change. We spent months (or more) tweaking the data model on Wikidata so that our imported data would properly represented. Once we were confident in the result (and only then), we reimplemented our gene/protein template as {{Infobox gene}} -- same presentation, but using data drawn from wikidata. This conversion was done in stages (completed ~ May 2016), and everything was announced and coordinated with WP:MCB.

In addition to adding gene/protein data to Wikidata, we are also interested in adding content related to human diseases and drugs. (This data has value for us even outside of its potential use on WP.) We have been importing data from commonly used sources in the biomedical research community. This process is still ongoing, and as for gene/protein data, it's also not a trivial process. The data modeling and the bot coding are both continually getting better, and we always appreciate input from both the WD and WP community on how to improve things. However, we have never made any claims about being fully confident enough for them to appear in templates like {{Infobox medical condition}} or {{drugbox}}. If we ever did want to propose using wikidata as a resource, we would certain to coordinate with WP:MED and/or WP:CHEM. Bottom line, we fully support the important oversight role that the wikiprojects play, and fully support applying a very critical eye to transcluding wikidata content. We take no offense if the verdict is that wikidata content is not mature enough yet, but we also ask not to be "blamed" anytime people outside of our team use wikidata content without consulting us or the relevant wikiproject. Cheers, Andrew Su (talk) 18:26, 24 January 2017 (UTC)[reply]

Does this work include {{Chembox}}, which intentionally overlaps {{Infobox drug}} (esp wrt identifiers and chemical/physical data)? -DePiep (talk) 18:37, 24 January 2017 (UTC)[reply]
Hi @DePiep: the chemical data that we are loading into wikidata certainly overlaps the fields that are contained in {{Chembox}} as well. But again, we haven't taken an active role in changing any template to use Wikidata content (with the exception of {{infobox gene}}). (I'm pretty sure you know this from discussions over at WT:CHM, but just to be sure!) If your question is whether I think caution should be exercised when transcluding content from wikidata here on WP and {{chembox}}, I think the answer is generally yes. If you let us know which fields you are interested in transcluding, we can comment on how stable things are (data model, data sources, and update cycle). Sound reasonable? Cheers, Andrew Su (talk) 00:38, 26 January 2017 (UTC)[reply]
Where is this Project being talked? For now, it feels like enwiki template development is being frozen into 'don't touch it, just wait'. You'll get this. (I have a serious data model for both {{Chembox}} and {{Infobox drug}} by chemical compound. How to check with this bot team?). -DePiep (talk) 01:25, 26 January 2017 (UTC)[reply]
We do most of our Wikidata discussions at WD:MB, and you are welcome to check in there about any issue in general or any data you want to transclude in specific. (Or even participate in our data loading/modeling, of course.) I think that would be a good first step before considering transcluding into well-established WP infoboxes. I hear and understand your frustration with the cautionary message. My concern of course is that we not move so quickly that the WD data is not properly vetted by WP standards, which I think would lead to long-term distrust. This is how I'm thinking about it, but of course would welcome your thoughts as well. Cheers, Andrew Su (talk) 06:51, 26 January 2017 (UTC)[reply]
I remain to have serious concerns about this. I have since we were talking about using WikiData for identifiers earlier run into other data that is being compared to WikiData. For one template (I would call it data 'of general public interest'), that concerns about 3000 datapoints, of which more than half are categorised as 'not the same as on WikiData'. That would suggest to me that at about 750 of those are wrong there, but that then also goes for the smaller half (the ones that are the same) .. it would mean that about half of them are plainly wrong. And this is data 'of general interest', not some specific database identifier in a corner of science. I would not expect the former to go wrong this much, on the other hand, database ids can be compared from official database files (we can download the whole of drugbank), which may give less problems.
Before we start transcluding, I think it is good to see numbers for 'how many we have here and they don't have there', 'how many they have there that we don't have here', 'how many have a different here and there', and 'how many are the same here and there'. The second category should not contain more than a couple of % of the total number .. otherwise transcluding from WikiData will make our situation significantly worse than what we have now (I agree, from the previous example, we may have 1500 wrong here as well - though for some identifiers I trust our data more as we actively looked at it, and if it is here, people will actually repair it because they don't have to figure out where to do it there - displaying becomes increasingly ugly if we have to include edit links to external wikis). --Dirk Beetstra T C 03:55, 26 January 2017 (UTC)[reply]
Great point. User:Sebotic started exactly such an analysis on PubChem IDs (I think discussed somewhere in the archives). We got distracted by other projects, but I think he will have it complete soon and will report results at WT:CHM. Cheers, Andrew Su (talk) 06:51, 26 January 2017 (UTC)[reply]
I saw the {{PubChem}} one as well, there are 36 (Category:PubChem ID (CID) different from Wikidata (33)) where Wikipedia is different from WikiData, meaning that at least one of the two is wrong - there are 36 mistakes together (out of 195 total transclusions). There are more cases (Category:PubChem ID (CID) same as Wikidata (103)) where they are both the same, or where WikiData does not have the data (Category:PubChem ID (CID) not in Wikidata (66)), but by extension, some of those must be wrong on both ends (and if they were copied from one place to another .. ). I have other of those statistics on my radar where the number of cases with different data is 20.600 (and where other, missing data is automatically pulled from WikiData ... and thát may be a BLP concern). --Dirk Beetstra T C 07:46, 26 January 2017 (UTC)[reply]
As Beetstra says. Last December I had in the sandbox for {{Chembox}} a setup that would categorize two pilot checks: A. articles with/out a QID (+link to WD item page inviting to edit). B. comparing & analyse (pilot datapoint) CAS Registry Number local input vs. Wikidata value. I stopped it because I get from Andrew Su's posts that we'd better wait nutil the bots have made the WD datra perfect or so. In short: I still have no clue on how the (respected) Bot and editors are supposed to improve this WD data & usage. (I think I am in line with Beetstra's remark; tell me if I mistake). -DePiep (talk) 10:11, 26 January 2017 (UTC)[reply]
@DePiep: - how much coding would it take to categorise CASNo on en.wikipedia into 'en=value;wd=empty','en=empty;wd=value','en=wd','en!=wd' (the rest of the transclusions of the chembox are then obviously empty) for the 'main CAS number' in the chemboxes? --Dirk Beetstra T C 10:56, 26 January 2017 (UTC)[reply]
And you are well in line with me :-) .. I want to add that I get a feeling that there is a huge push from WD along the lines of 'we took a lot of data from you guys, and we worked hard on it, it is now time that you use it back ... --Dirk Beetstra T C 10:58, 26 January 2017 (UTC)[reply]
Not much coding, I was working on that in sandboxes. I also wanted to get these categories right from the start (like cat naming pattern, useful subdivisions). Then there is this topic we better discuss too: the data model for a Chemical page (~= having {{Chembox}} or {{Drugbox}}). In short, article could be: chemical substance (e.g. a group), chemical compound (what we think of first), with multiple chem compounds (by indexes CASNo1), vaccine/mab (drugs only). One cover-all parameter for this (to improve specific categising)? Because: when we have an article without CAS number, the maintenance task depends: CAS number is missing, not assigned, or doesn't exist because it's a chemical group etc. Also, I'd like to categorise articles by "having a QID" or not (no QID=not in WD!).
Those maintenance categories are a huge invitation to edit WD (or the en:article) of course. It's just, I keep getting mixed signals from Andrew Su on whether we should start this route here on enwiki. Sounds like we would interfere with the bot process. A simple answer possible, Andrew Su?
re 2nd part: Good! -DePiep (talk) 14:45, 26 January 2017 (UTC)[reply]
IOW Beetstra, I'm ready to dive into the sandboxes again, and make formal talking points/proposals for this. And indeed, categories as you mention. -DePiep (talk) 14:48, 26 January 2017 (UTC)[reply]
Thanks to you both. I actually wasn't aware of those categories that highlight differences between WP and WD -- good idea. Once Sebotic updates his analysis script and results, we'll report here and figure out together the best path moving forward. Regarding DePiep's comment about editing WD, my recommendation would be to go ahead and change WP if WD is right. If WP is right and WD is wrong, go ahead and change WD if you like, but most important would be to pass along those examples to our team. Ultimately we want to make sure our upload and synchronization bots on WD are perfect relative to the sources, so we need to examine the edge cases to figure out where things are going wrong. Cheers, Andrew Su (talk) 19:20, 26 January 2017 (UTC)[reply]
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