Template talk:Chembox

Discuss converting to use {{infobox}}

So I wanted to start a discussion about converting this template to use {{infobox}} as a base. As I see it, there are a few options:

1. Convert this to use {{infobox}} as a base, which will change the look of the box but unify it to the style of 99% of the infoboxes
2. Create a custom Module that will exactly replicate the look of the current box.

Looking for thoughts and input! --Zackmann (^{Talk to me}/_{What I been doing}) 00:47, 7 October 2018 (UTC)

IMO it is poinntless to create a mimicking module. Better: create a module that reads the parameters and then feeds them into Module:Infobox. Don't bother keeping the |SectionN= parts: when the infobox is ready have a bot edit the pages (remove Section subtemplates not their parameters). - DePiep (talk) 08:19, 7 October 2018 (UTC)

• question This showed up on my watchlist, and maybe this out of my bailiwick so I might be missing something, but what exactly is the problem that this is proposal in meant to solve? Yilloslime (talk) 16:54, 9 October 2018 (UTC)

Using {{Infobox}} instead of the wikitable as it is now would produce a great infobox, both in view and in websitebasics (good use of css, semantics, etc). Also, we'd get rid of the cumbersome subsections and subtemplates required. (However, must say current wikitable setup did allow for easy adjustments wrt new data rows etc.). -DePiep (talk) 17:02, 9 October 2018 (UTC)

@Zackmann08: - Its a huge project to convert with an enormous amount of parameters "hidden" in the same number of subtemplates (or more). But IMHO you (and others) should be welcome converting it. I would sugges making a template:chembox/new (or something similar) and afterwards, converting all the articles to use the new one. The current version is a pain in the *. E.g. if you want to move e.g. conjugate acids from "Properties" to "related" you have to change the template (obviously) but also change all the articles. But first you have to figure out the name of the subtemplates, etc. Christian75 (talk) 10:03, 15 October 2018 (UTC)

True, Christian75, but a bit moot. I have been maintaining this one for over 5 years, and always have been able to make such changes when agreed upon (actually, there were very few). Many more times this change was made: add a parameter; add index to parameter. PLus of course updatres to paramewters like external database link formatting. I do not think this is the bottleneck. -DePiep (talk) 15:43, 15 October 2018 (UTC)

@Zackmann08: I would not necessarily be opposed to this, but can you please update us on how much work this would be (after conversion of the template, which in itself will be a lot of coding). The current system uses sub-templates as modules, I presume that a infobox-based system would not do that. That would mean 10.000+ edits to convert all pages. Coming from that is that then the grouping would get lost (all parameters are feeding into the main template, though they could be grouped on the page, that is then not necessary and could become a pain to maintain). So basically, if we can keep the same sectioning system as we have now, then I would be in favour, otherwise I likely oppose that change due to the loss in organisation. --Dirk Beetstra ^{T C} 10:12, 15 October 2018 (UTC)

Question: Will this change how we edit chembox? Despite it appearing on a lot of pages I don't think there are a lot of editors who regularly interact with it. It's taken me a lot time to learn all its secrets. It would be a bother to have to start learning it all over again. --Project Osprey(talk) 12:54, 15 October 2018 (UTC)

@Beetstra, Project Osprey, and Zackmann08:. {{Chembox}} today has some 560 parameters (of whitch: 118 element symbols, 54 image-related, 120 indexed like |CASNo1=, and so 270 regular others).

A new chembox (preferred name: {{Infobox chemical}}) would a. use Module:Infobox and b. be Lua-programmed not wikitext. I strongly advise not to program directly in {{Infobox}} (like {{Infobox drug}} is) because of number and complexity (relatedness) of the parameters. INstead, create a new module that reads the parameters more systematically (recgnising indees & image indexes?), and then feeds them into module:infobox.

Both for coding ease and for article editors: the new template handles exactly the same parameters and will show the same structured infobox (order of parameter-values, section headings, ...). Expect makeup being slightly different (like: a bulleted list may appear).

I predict that the pressure for piggyback changes will appear, but should be denied ("while we are at it, let's change this parameter name" etc.).

The new template will not use |SectionN= structure. Once tested & stable, a bot can change all 10k pages (that is what bots are for) like this, but *not* parameter names & input:

Switchover to new template (demo bot edit)

{{<s>Chembox</s>Infobox chemical<!-- use new template --> | Watchedfields = changed | verifiedrevid = 464364488 | ImageFileL1 = Ammonia-3D-balls-A.png | ImageNameL1 = Ball-and-stick model of the ammonia molecule | ImageFileR1 = Ammonia-3D-vdW.png | ImageNameR1 = Space-filling model of the ammonia molecule | ImageFile2 = Ammonia-dimensions-from-Greenwood&Earnshaw-2D.png | ImageName2 = Stereo structural formula of the ammonia molecule | IUPACName = Azane | OtherNames = Hydrogen nitride, Trihydrogen nitride, Nitrogen trihydride <s>|Section1={{Chembox Identifiers</s> | InChI = 1/H3N/h1H3 | InChIKey = QGZKDVFQNNGYKY-UHFFFAOYAF | CASNo = 7664-41-7 | CASNo_Ref = {{cascite|correct|CAS}} | PubChem = 222 | ChEMBL_Ref = {{ebicite|correct|EBI}} | ChEMBL = 1160819 | ChemSpiderID = 217 | ChemSpiderID_Ref = {{chemspidercite|correct|chemspider}} | UNII = 5138Q19F1X | UNII_Ref = {{fdacite|correct|FDA}} | EINECS = 231-635-3 | UNNumber = 1005 | KEGG = D02916 | KEGG_Ref = {{keggcite|correct|kegg}} | MeSHName = Ammonia | ChEBI_Ref = {{ebicite|correct|EBI}} | ChEBI = 16134 | RTECS = BO0875000 | SMILES = N | StdInChI_Ref = {{stdinchicite|correct|chemspider}} | StdInChI = 1S/H3N/h1H3 | StdInChIKey_Ref = {{stdinchicite|correct|chemspider}} | StdInChIKey = QGZKDVFQNNGYKY-UHFFFAOYSA-N | Beilstein = 3587154 | Gmelin = 79 | 3DMet = B00004 <s>}}</s> <s>|Section2={{Chembox Properties</s> | Formula = NH<sub>3</sub> <s>}}</s> <!-- etcetera--> }}<!-- end of template -->

This answers the question by Project Osprey: No, no change in editing because the same parameters are available. More easy: no need to dig into what subsection/subtemplate you must add for |OtherCations=.

After the moveover is complete, proposals can be made to change the template in whichever way. -DePiep (talk) 16:21, 15 October 2018 (UTC)

Thank you for clarifying that. I don't think these changes will effect me in anyway, thus I shouldn't have a role in approving them, but I certainly don't have any objections. Good luck. --Project Osprey (talk) 20:18, 15 October 2018 (UTC)

And that is now exactly the problem I have user:DePiep:

Beetstra demo: risk of random parameter ordering

{{<s>Chembox</s>Infobox chemical<!-- use new template --> | RTECS = BO0875000 | Watchedfields = changed | StdInChIKey = QGZKDVFQNNGYKY-UHFFFAOYSA-N | Beilstein = 3587154 | verifiedrevid = 464364488 | N = 1 | ImageFileR1 = Ammonia-3D-vdW.png | KEGG = D02916 | ImageNameR1 = Space-filling model of the ammonia molecule | ImageFile2 = Ammonia-dimensions-from-Greenwood&Earnshaw-2D.png | ImageName2 = Stereo structural formula of the ammonia molecule | OtherNames = Hydrogen nitride, Trihydrogen nitride, Nitrogen trihydride | InChI = 1/H3N/h1H3 | InChIKey = QGZKDVFQNNGYKY-UHFFFAOYAF | CASNo = 7664-41-7 | SMILES = NH | PubChem = 222 | ChEMBL_Ref = {{ebicite|correct|EBI}} | N = 3 | ChEMBL = 1160819 | ChemSpiderID = 217 | UNII = 5138Q19F1X | UNII_Ref = {{fdacite|correct|FDA}} | ImageFileL1 = Ammonia-3D-balls-A.png | EINECS = 231-635-3 | UNNumber = 1005 | KEGG_Ref = {{keggcite|correct|kegg}} | MeSHName = Ammonia | CASNo_Ref = {{cascite|correct|CAS}} | ChEBI_Ref = {{ebicite|correct|EBI}} | ChEBI = 16134 | SMILES = N | H = 3 | StdInChI_Ref = {{stdinchicite|correct|chemspider}} | StdInChI = 1S/H3N/h1H3 | ImageNameL1 = Ball-and-stick model of the ammonia molecule | StdInChIKey_Ref = {{stdinchicite|correct|chemspider}} | ChemSpiderID_Ref = {{chemspidercite|correct|chemspider}} | Gmelin = 79 | 3DMet = B00004 | IUPACName = Azane <!-- etcetera--> }}<!-- end of template -->

will be totally valid, and for ammonia, benzene, water, etc. an organisational hell to maintain. There are 560 parameters, and on some pages we might have > 150 in use. Unless they are enforced structured in groups, we will notbe able to maintain that, and n00by editors will get lost in the soup (there is N=1 in the top, let me add H=3 below it).

If we can keep the same modular approach in the article, but an infobox LUA module to display it, then fine. --Dirk Beetstra ^{T C} 04:18, 16 October 2018 (UTC)

To be clear: the new infobox will of course show values in a fixed order, grouped in subheaders as we like (as Chembox does today). The only change is: no hard requirement to add parameters in their own subtemplate/subsection. Not having to research those (9) subtemplates for parameter editing I call an advantage (less enforced requirement to study documentation).

The only possible disadvantage I can think of now is, indeed, that in the edit screen all parameters can be in random order, as Beetstra points out (unless 'maintenance is about code & bot maintenance? -- then please refine). Today, they "only" can be random within their own subtemplate (parameters per subtemplate: main=60, Identifiers=77, Properties=65; my experience is that they most often follow /doc sequence; why not). To help this editor's chaos away I can think of: 1. In /documentation present blank param list in standard order; use <-- comment --. as grouping titles (see {{infobox drug}}), ask the switchover bot to order all params, search for more editor's support into this (VisualEditor, TemplateData, new gadget, addordering to WP:AWB, ...) to keep them organised.

Yes this order might become too random in incidental siatuations, but no IMO the enforced grouping is too much a negative now and surely should not prohibit using {{Infobox}}. -DePiep (talk) 05:07, 16 October 2018 (UTC)

I am just thinking (hoping?) that we can actually keep the structure as I believe it helps in maintaining (as you say, most 'new' chemboxes are created by copying the empty templates out of documentation, or by copy/paste and adapting from other pages). The 'logic' makes it IMHO easier to find the parameters you need (which are not 'standard'), then that it has to come out of a large list (where in the /doc, they would still be grouped. Can we use the same in-document code, but make the subtemplates pass everything through to the top level? That also avoids that we need to bot-edit 10.000+ articles for implementation. --Dirk Beetstra ^{T C} 06:23, 16 October 2018 (UTC)

(correction needed? Beetstra: something wrong with this? In your demo you wrote "...will be totally valid", but actually you added |N=1, |N=3, |H=3 [1]. But that's repetition of |N=: duplicate parameter. Then I tried to "fix" it by changing the second N into an H -> same sort of error duh; I revert right now. I suggest you fix it into what you wanted to show. -DePiep (talk) 15:44, 16 October 2018 (UTC))

@DePiep: That was my point exactly (the errors are intentionally) - In a list of 50 parameters, one needs to carefully check for that (though a module could tell you of such conflicts). It is much easier when the data is forcefully grouped as we have it now, and you end up with 10-15 per group. --Dirk Beetstra ^{T C} 05:37, 17 October 2018 (UTC)

Note: it is valid, the current system would take, IIRC, the last value you provide, just ignoring the last one. --Dirk Beetstra ^{T C} 05:38, 17 October 2018 (UTC)

OK, example of unintended but confused behaviour then. But I note that a repeated parameter a. gets a meggaage in preview, and b. is listged in Category:Pages using duplicate arguments in template calls. This is the part not "...will be totally valid". -DePiep (talk) 06:00, 17 October 2018 (UTC)

Nomination of 3DMet for deletion

A discussion is taking place as to whether the article 3DMet is suitable for inclusion in Wikipedia according to Wikipedia's policies and guidelines or whether it should be deleted.

The article will be discussed at Wikipedia:Articles for deletion/3DMet until a consensus is reached, and anyone, including you, is welcome to contribute to the discussion. The nomination will explain the policies and guidelines which are of concern. The discussion focuses on high-quality evidence and our policies and guidelines.

Users may edit the article during the discussion, including to improve the article to address concerns raised in the discussion. However, do not remove the article-for-deletion notice from the top of the article.

Deletion of this artice would give {{Chembox}} a redlink in the lefthand side. DePiep (talk) 15:26, 15 October 2018 (UTC)

Parameter: talk central is here

Following the AfD for article "3DMet" (still open), I published a talk post Removal of parameter |3DMet= 3DMet from {{Chembox}} in several places. To be clear: that is not about the AfD itself, but about a consequence of AfD-3DMet-deletion. This postings invoked separate talks, which is bad. So I say: topic "Deletion of data-row 3DMet from {{Chembox}}" is to be performed here, from now on. I'll try to merge the posts. -DePiep (talk) 19:33, 19 October 2018 (UTC)

Removal of 3DMet data from {{Chembox}}

At the moment, the article about 3DMet (one in the Category:Chemical databases (49)), is up for deletion (AfD). Reason is lack of WP:NOTABILITY, as measured by ~not being referenced in secondary (independent) sources. IOW, virtually no sources refer to it as useful etc. or actually use 3DMet.

If and when this article is deleted, it follows that the {{Chembox}} data row (|3DMet= in {{Chembox}}) should be removed too (we should not link or point to an irrelevant and not-notifyable database). Today, some 126 articles use parameter |3DMet=: [2].

The only way to save this information is to prove notability of 3DMet by adding secondary sources (read the AfD though for an investigation already made into this: few sources are sound).

Parameter was added in 2007. ping @Graeme Bartlett and Beetstra:. -DePiep (talk) 07:19, 19 October 2018 (UTC)

If there is no article, we don't have to delete the template links. Instead a Wikipedia:3DMet page could be the target. We can keep the 3DMet info in the Chembox as long as it is useful. Graeme Bartlett (talk) 11:13, 20 October 2018 (UTC)

When the database itself is considered not encyclopedic, its data has no place in Wikipedia content space. Can't have it both ways. Linking to non-content space like Wikipedia:3DMet would be like linking to a help-page, or how-to-page, or WP:NOTEVERYTHING, WP:LINKFARM. -DePiep (talk) 12:43, 20 October 2018 (UTC)

If the article on 3DMet is deleted because it is insufficiently notable to warrant an article, that is entirely independent of whether we can use data from it or not. The two decisions should be made separately. -- Ed (Edgar181) 14:06, 20 October 2018 (UTC)

How so? I repeat, if the database is irrelevant, how can its data be relevant? And, if we write "3DMet ID = xxx" in the article (as we do now), how can it be that there is nothing to answer "What is 3DMet?". -DePiep (talk) 14:13, 20 October 2018 (UTC)

If the article on 3DMet is deleted because it is deemed insufficiently notable to warrant a Wikipedia article, that does not automatically render the database irrelevant. Arguments presented at the AFD can be considered when making a decision about whether to keep 3DMet in the chembox, but the AFD does not dictate an automatic course of action in that regard. If we decide to keep 3DMet in the chembox and there is a pressing need to answer the question "What is 3DMet?", I'm confident in our ability to provide an answer. -- Ed (Edgar181) 14:22, 20 October 2018 (UTC)

I agree that AfD can not automatically delete the chembox data row, but by logical reasoning it does. As the AfD discussion points out, there are no sources (publications) actually using 3DMet data. If we keep the data in the articles, that would be sort of nice-to-have information, but nothing encyclopedic by definition. Yet we are not a toolbox. (TBH, personally I had to swallow the appearing outcome of the AfD, but also must be tough on what it means. I prefer not to have trivial non-info in the infobox). -DePiep (talk) 14:38, 20 October 2018 (UTC)

Idea: the 3DMet ID can be added and saved in Wikidata. WD seems to be less strickt in Notability. -DePiep (talk) 14:42, 20 October 2018 (UTC)

To be clear: No 3DMet article, no related |3DMet= sub-data in {{Chembox}}. -DePiep (talk) 22:41, 23 October 2018 (UTC)

I still don't see the case for this. We can cite a book which doesn't have an article. We can cite a scientific journal that doesn't have an article. We do these things all the time. Why should a database be any different? XOR'easter (talk) 16:36, 24 October 2018 (UTC)

First, linking to an external 3DMet item is not a citation (not a reference source for an encylopedic statement). Then, assuming the AfD closes as delete for missing notability: it is a link to external information -- information that is, by not being relyably cited itself elsewhere, deemed not relevant nor notable. - DePiep (talk) 17:08, 24 October 2018 (UTC)

There might be a reasonable argument that material from a database without its own article is providing the wrong weight to information from that database. I don't know if I per se agree with that argument (and I might waffle on it depending on the specific source in question), but that's probably the direction of discussion you might take. --Izno (talk) 17:19, 24 October 2018 (UTC)

"First, linking to an external 3DMet item is not a citation (not a reference source for an encylopedic statement)" — true, in a strict sense of the word "citation", but they seem morally equivalent to me in the present context. If we'd be fine with using 3DMet as a footnote, then it's hard to object that strongly to including a link in an infobox.

I agree that there might be an issue with undue weighting, but I don't think a line in an infobox really counts as that much weight.

I asked at the deletion discussion page but got no reply, so I'll raise the question again here: Is there some article into which the one on 3DMet can be merged? (Cf. how when journals are not quite notable, we redirect to the publisher, university or society that runs them.) I think the peer-reviewed references we were able to find about 3DMet would be plenty to support a short paragraph in some other article, to which 3DMet could be a redirect. XOR'easter (talk) 18:24, 24 October 2018 (UTC)

re XOR'easter. I can follow your line wrt external linking & sourcing, but in this case 3DMet has been explicitly put to the test of being noteworthy (result: it failed). No secondary scientific sources refer to it, as was researched for the AfD. That says, at least to me: it has no scientific relevance. Were the database scientifically useful and adding information in any study on chemicals, that study would have reported it ("We have used 3DMet to compare these properties for substances x, y, z"). But these substance-specific sources neither did show up. Were there a proposal today to newly add 3DMet to the infobox, the same questions about relevance would be asked and so far unanswered. It appears 3DMet is more like a tool for research, not a data source that adds new data to a research. As a tool, it does not end up in the publications (nor does: "We analysed the data with spreadsheet MS Excel"). So far, I have not read a convincing argument on what the 3DMet link does add. Most advocates mention like 'useful', but that would be either WP:OR or usefulness as a nice-to-have tool.

On describing 3DMet in a suitable paragraph: could be possible, but I did not develop that option myself because I created the article 3DMet and so I might be too involved (I myself do not want to look like cicumventing the AfD; probably others could -- but doesn't it say something that it is not obvious to work that out?). -DePiep (talk) 06:59, 25 October 2018 (UTC)

There's a difference between being "notable" in Wikipedia's particular sense of that word and being "noteworthy". Wikipedia's meaning of "notable" is more like "article-worthy". The standard for including a datum in an article is different from the standard for creating an entire article. For example, Isaac Newton is notable, in the Wikipedia sense. Suppose that when he stayed in London, he habitually rented a room in a particular boarding house. That building might or might not be Wikipedia-notable — perhaps nothing has been written about it, apart from "Isaac Newton slept here". So, we might not be warranted in having an article about the house, but we could still mention it in a biographical article about Newton. XOR'easter (talk) 15:40, 25 October 2018 (UTC)

I would like to note that the 3DMet ID has plenty of information that no other identifier has; one example is its data point on globularity. 3DMet has information that people might come looking for but can't find, and so linking is helpful. As such, I would be in favor of keeping the template's line.

So what of the question of linking? If deletion of the 3DMet article is denied or if 3DMet's information can be merged into a new article-- "List of chemical databases" or something along those lines-- then by all means link to to that Wikipedia! But if that can't be done, why not link to http://www.3dmet.dna.affrc.go.jp/, the databases's main page? 50.39.171.4 (talk) 00:42, 25 October 2018 (UTC)

As I wrote to XOR'easter above: if it has scientifically relevant and even unique information, it should and would have shown up in soureces. Not just sources about the database, but in sources that reseach certain compounds. But alas, the AfD shows not even that. So it is more like a tool not a information source. Useful, but not adding scientific relevance. Note that this info is in the WP:INFOBOX in the lede, so we must be tough and self-critical.

In WP:EXTERNALLINKS I could not find a convincing rule to include this data. In general, an EL in article body may not be added lightly. - DePiep (talk) 07:05, 25 October 2018 (UTC)

I didn't realize that general rule. Thanks for the clarification. 50.39.171.4 (talk) 20:39, 25 October 2018 (UTC)

I would tend to agree that a single link probably is not obtusely weighted. (I have a general problem with external links in infoboxes, but I don't feel like being uppity about that here as I think it's a broader discussion.) --Izno (talk) 18:59, 25 October 2018 (UTC)

Weird ref format

See Sodium bromite: data "3Dmet 3D JSmol model" has ref links in its left? "[3][4][5]: Interactive image"-DePiep (talk) 23:10, 4 November 2018 (UTC)

Template needs |SIMLES_ref= to differentiate from current |SIMLES_Comment=, used differently in SMILES and JSmol. Temporally ~solved in the article. -DePiep (talk) 08:36, 17 November 2018 (UTC)

Add MetaCyc identifier in the list of Identifiers for Compounds

We would like to add MetaCyc identifier in the list of Identifiers for Compounds. MetaCyc is highly curated database. The links to MetaCyc already exist from the EC numbers for example:https://en.wikipedia.org/wiki/Pyridoxal_oxidase. How can I add these links? — Preceding unsigned comment added by Anko04 (talk • contribs) 18:33, 5 November 2018 (UTC)

What would be the addition, information-wise spoken? MetaCyc does not have much secondary sources, so ity might be up for deletion (like we had for 3DMet recently). Also, who is "we"? -DePiep (talk) 18:47, 5 November 2018 (UTC)

Hi, "we" are the group that created MetaCyc and continues its curation on an ongoing basis - the Bioinformatics Research Group at SRI International. We believe that adding these links to MetaCyc compound pages will be very beneficial to Wikipedia users. Unlike many other compound databases (e.g. ChEBI), MetaCyc compound pages, in addition to the usual details, also contain all of the biochemical reactions that the compounds are known to participate in. For example, if you go to the L-tryptophan page (https://biocyc.org/compound?orgid=META&id=TRP#tab=showAll) and scroll down, you will see many dozens of reactions in which L-tryptophan participates. Those reactions are hyper link, so it only takes one more click to see a full diagram of the balanced reaction, including atom mapping between the reactants and products. To the right of each reaction, if applicable, is a hyperlink to a pathway in which the reaction participates. If you scroll even further down, you will find a list of all the enzymes of which L-tryptophan is known to be an effector (e.g. an inhibitor), followed by the relevant references. In short, we really think that linking to compounds in MetaCyc will provide a lot of additional information that is not easily obtained otherwise. Rcaspi (talk) 21:52, 5 November 2018 (UTC)

I find the question still appropriate, but first a bit unfriendly necessary notice. I must note possible COI's wrt the MetaCyc topic. Rcaspi, Pkarp11, Anko04 are notified on their talkpage. This may sound unwelcoming, but as WP:DISCLOSE describes this is for encyclopedial integrity, not distrust. I note that you are open about this relationship with MetaCyc. -DePiep (talk) 07:00, 6 November 2018 (UTC)

Some considerations. We have Category:Biological databases (452), Category:Chemical databases (49) articles in WP. Also, outside ar hundreds (thousands?) more. We can and should not add all these as external links, let alone in the infobox (in top) that {{Chembox}} is. We are not a linkfarm, not a directory, not an indiscriminate list of info. I am not claiming here that MetaCyc is one of those, but we must check inclusion of MetaCyc data it against these standards (as with other external links). Also, it is/would be an external link, not information or a source for article body text information. That requires more additional value to be included.

Similarities 3DMet: recently, we have removed the article 3DMet for lack of notability (discussion here), but somehow not its external link in {{Chembox}} (discussion here). I am still not convinced that link should be kept, and similar reasoning could apply here.

It is up to the WP:CHEMISTRY, WP:WikiProject Biology-related WikiProjects, ... community here to flesh out this criteria.

About Wikidata: meanwhile, one could consider adding the property to Wikidata (MetaCyc (Q692423)) as MetaCyc ID (3DMet ID example added in the box here). This is an independent route (independent of {{Chembox}} including), and might be more appropriate for automated mass editing, maintenance and publishing (for example, in the future a Wikidata-generated external link list could be included in compound articles).

Tech questions: which identifier does a compound have, and is there a URL-formatting line to get to a compond's item page (API)? -DePiep (talk) 07:28, 6 November 2018 (UTC)

Found the API introduction. Relates to BioCyc and EcoCyc. -DePiep (talk) 07:35, 6 November 2018 (UTC)

LOL Asking for directions: Q: How to get the object ID to link to?" A: "The easiest way to get the object ID is to just go to the the web page that you want to link to and copy the URL from there". -DePiep (talk) 17:21, 6 November 2018 (UTC)

More on tech: link (below) is dead, maybe [3]. I also would like to learn what is the relationship between BioCyc, EcoCyc and MetaCyc. Especially why we should add a MetaCyc ID link, but not the others. (I'd expect to use the most general database). BTW, the link is dead but maybe biocyc homepage is an entrance. It looks like there are two identifiers: for example L-tryptophan has "META" and "TRP". -DePiep (talk) 08:15, 11 November 2018 (UTC)

Let me try and address the concerns that you have raised. First, concerning COI: as you pointed out, we do not try to hide who we are. We believe that adding these links will be useful for Wikipedia users, and to the best of our understanding there isn't an ethical problem that should prevent us from initiating this process.

Regarding why add links to MetaCyc and not to the hundereds of other chemical databases: note that MetaCyc is somewhat unique in being not just a chemical compound database, but also a reaction and metabolic pathway database. Thus it provides a lot of additional yet relevant information for chemical compounds compared with a plain chemical compound database, even if the latter is an excellent resource such as ChEBI. The only similar resource available to my knowledge is KEGG, which by the way is included in Chembox. Yet, KEGG does not have the visual clarity that exists in MetaCyc (color-coded fully balanced reactions with the full structures of the compounds, including atom mapping), and KEGG contains less reactions that MetaCyc. So I repeat my initial motivation - links to MetaCyc will indeed enrich the data content available to Wikipedia users, in ways none of the other hundreds (or thousands) of chemical databases can provide.

I would also point out that MetaCyc has been around for a very long time (started in 1998) and has become a very well known and heavily used resource. In the discussion about 3DMet I find "The journal article introducing 3DMet has only 10 citations on Google Scholar and 4 on Web of Science, compared to 1,015 GS citations and 683 by the publisher's database for the journal article introducing PubChem." The articles describing MetaCyc have been cited over 2500 times, far more than PubChem (I can provide the list if required). Besides, important databases such as ChEBI, ExplorEnz (the Enzyme Commission database) and Uniprot already link to MetaCyc.

Regarding your tech question: To ensure the link is live, I will an example: the URL for compound with id "TRP" is [4]. As for how to get the IDs - I can see why you are laughing at the comment from the web page, but keep in mind that this was meant for people who want to link to just a few items, and do not want to spend time figuring out how to do it systematically. There are several ways to get the MetaCyc compound IDs. One way is to download a SmartTable of all compounds from MetaCyc, which would include the compound name, its MetaCyc ID and any other fields you may specify, such as IDs in other databases. There is also a metabolite translation service at https://metacyc.org/metabolite-translation-service.shtml where one can submit a list of compounds using names, IDs in other databases etc and get the MetaCyc ID back. When it comes to that, we should be able to help with the mapping. Rcaspi (talk) 18:45, 6 November 2018 (UTC)

More tech remarks above. -DePiep (talk) 08:15, 11 November 2018 (UTC)

More answers: I know all these Cyc's can be confusing, so here is an explanation. MetaCyc is a general database of metabolism from all organisms. It has by far the most compounds/reactions/metabolic pathways, as those are assembled from published information gathered from bacteria, archaea, fungi, plants, and animals. MetaCyc is used by the Pathway Tools software to infer the metabolic network of organisms with a sequenced genome, generating a specific Pathway/Genome Database (PGDB) for each one. The collection of the (currently more than 14,000) PGDBs is named BioCyc. So each BioCyc PGDB has only a subset of the compounds, reactions, and pathways that are found in MetaCyc, which is relevant for the specific organism (but in addition has the genomic information of that organism, something MetaCyc does not have). Thus, it makes sense to link chemical compounds only to MetaCyc, because it has the richest collection of this data. EcoCyc is just one of the 14,000 PGDBs in BioCyc, for E. coli K12. It stands out because it is arguably the best-curated database for any organism, having been manually curated for many years by many curators. Rcaspi (talk) 21:25, 21 November 2018 (UTC)

I ask all WikiProject participants to judge this request: does adding the external link to MetaCyc (or BioCyc, EcoCyc) add relevant information? -DePiep (talk) 08:26, 11 November 2018 (UTC)

Content arguments are in paragraph "Regarding why add links to MetaCyc ...". -DePiep (talk) 08:32, 11 November 2018 (UTC)

Converting template to use Template:Infobox

The following discussion is an archived record of a request for comment. Please do not modify it. No further edits should be made to this discussion. A summary of the conclusions reached follows.

Initiator has apparently decided they are not interested in having this discussion, as they removed it[5] with the comment "nevermind". DMacks (talk) 12:11, 24 November 2018 (UTC)

---

Should {{Chembox}} be converted to use {{Infobox}} as a base?

I wanted to initiate a discussion about converting this template over to use the standard layout provided by {{Infobox}}. There are a number of reasons for this change:

• {{Infobox}} is one of the most widely used and well documented templates on here.
• This change would make the infobox much easier to maintain and improve on over time
• {{Infobox}} conforms much better to MOS:ACCESS including issues with displaying on mobile devices.
• {{Infobox}} provides a standard and consistent look and feel across all infoboxes on the wiki. {{Chembox}} is one of the last remaining Infobox style templates that is not using {{Infobox}} as a base.

A couple of points that I want to emphasize right off the bat.

NO information would be lost.

As far as I'm concerned any implementation/conversion that would result in ANY data being lost is a non-starter. This discussion is 100% about restructuring and redesigning the layout so that it is more user friendly. If anyone (myself included) feels that there is some information that should be added to or removed from the infobox, that is fine but that should be a separate conversation and not part of this discussion. This includes things like auto-conversion and auto-categorization. The ONLY change I am talking about is to the layout. Other than that, there should be no functional changes as part of this RFC.

It is too much work is not a valid objection.

In a number of these discussions I have seen people object to a proposal simply because it will require too much work. I feel very strongly that this is not a valid objection. If you feel it is too much work, then you do not need to participate. However, if you are worried that because of the amount of work involved, something might be broken, that IS something to bring up, but please be specific about your concerns.

It could break is also not a valid reason to object.

Similarly the concern that it could go wrong is not a reason to object to the entire process. IF this process were to move forward, there would be a large number of people involved and we would all work together to make sure that nothing breaks. So please don't object to the proposal just because you are worried something might go wrong. If you have concerns, ABSOLUTELY raise those concerns! Part of the reason I am doing this as an RFC instead of just building the template is that I want to and need to hear from other people. There is no way I can envission all the issues myself. So, for example, please don't say "I object to the proposal because I'm worried it will break pages with <some characteristic>". Instead, if you support the change but are concerned that it will break stuff, it would be very helpful to say "I support this change as long as we consider the case of <some special case here>".

I am very interested in hearing opinions on both side of this, that is both people in favor of changing the format and those opposed to doing so. My one request is whatever side you are on, please be specific in your feedback. For example, don't say "Kill it! Time to eliminate this cruddy layout". Instead say "{{Infobox}} is much more userfriendly and would add value to this template." Likewise if you object, don't just say "If it ain't broke don't fix it", say "I'm concerned that if we try to convert such a complex template ______ may happen."

If you have any questions, comments or concerns for me directly, please don't hesitate to either {{ping}} me below or post on my talk page! Looking forward to a good discussion. --Zackmann (^{Talk to me}/_{What I been doing}) 21:03, 16 November 2018 (UTC)

The proposal - {{Chembox}} should be converted to use {{Infobox}} as a base and moved to {{Infobox chemical}}

Please post your comments below!

Comments

• @Zackmann08: What is your brief and neutral statement? Please observe how it appears in the RfC listings. Remember that Legobot copies everything from the {{rfc}} template down to the next timestamp. --Redrose64 🌹 (talk) 00:24, 17 November 2018 (UTC)
• I don't get how this is an RfC. Nobody would disagree. (BTW, this suggestion has been discussed before, e.g., one month ago, initiated by... Zackmann08). Actually, this is a "how to" question, which better be left to engaged & involved editors (not armchair RfC commenters). Worse is this: the wording "should be" is commanding sense, and for this I would not step into a multi-month multi-issue multi-editors task because of the risk of being commanded to do certain things. In short: this conversion should be initiated by involved, hands-on editors only, without outside 'you should do' interference. The better track I envision is a strong cooperation, heavily using a talkpage, not an RfC. -DePiep (talk) 00:53, 17 November 2018 (UTC)

@DePiep: I am more than happy to withdraw the RFC... I wasn't trying to cause problems. Was actually trying to do things the right way... I've been getting all sorts of flak for my work on {{Geobox}} because I'm not asking for enough input from others. If you'd like me withdraw the rfc I'm happy to do that. --Zackmann (^{Talk to me}/_{What I been doing}) 00:55, 17 November 2018 (UTC)

Invalid RfC, no clear question asked. Aow chembox makes use of subtemplates in a specific way, if that structure cannot be maintained I am against conversion. Don't fix things if it isnotbroken. --Dirk Beetstra ^{T C} 04:29, 17 November 2018 (UTC)

@Beetstra: first of all there was a clear question asked... The question was Should {{Chembox}} be converted to use {{Infobox}} as a base?. Second, you clearly didn't read the RFC because you just did exactly what the RFC said NOT to do which was to use a completely erroneous argument. No one is suggesting creating a template that cannot be maintained. You literally quoted the exact phrase that said not to use "if it ain't broke don't fix it". That misses the point completely and doesn't address the question. --Zackmann (^{Talk to me}/_{What I been doing}) 05:49, 17 November 2018 (UTC)

The discussion above is closed. Please do not modify it. Subsequent comments should be made on the appropriate discussion page. No further edits should be made to this discussion.

Convert to Infobox (for realz this time)

Howdy all! So after some consideration, I'm seriously considering working on converting this over to use {{Infobox}}. I want to see who might be interest in helping out with this process? There are 2 main things we will need:

1. People willing to help write test cases to compare {{Chembox}} to the new converted solution
2. People willing actually dig in and write code for the new solution

Couple of things I want to make clear to all those concerned:

1. No changes will be rolled out until consensus is reached! I don't want anyone concerned that they are going to login one day and find a radically changed template. No way that will happen.
2. This will definitely be a long process. Anyone who has looked at this template knows it is a complicated one. This will not happen overnight!
3. Everyone will have a chance to weigh in. Right now I'm basically looking to build a task force. Hopefully I can get 10-20 people together who are willing to commit some time to this. That being said, once a working proof of concept has been made, I plan to SLOWLY roll it out giving anyone and everyone a chance to weigh in a raise concerns.
4. You don't have to join the task force to raise concerns. Finally, I want to be clear, if you don't join the task force, that doesn't mean you don't get to weigh in! ANYONE can raise concerns. The taskforce is just going to be people who are willing to devote time to addressing the concerns raised and implementing them.

So to summarize, right now just looking to get some names of people who are willing to join the not-yet-named Chembox taskforce. If you have concerns about the entire process, please make some notes, but right now, if possible can we just discuss who wants to be part of the process?? Thanks all!! --Zackmann (^{Talk to me}/_{What I been doing}) 18:14, 20 November 2018 (UTC)

I'll help. I'm not the best with templates, but I'm decent. — AfroThundr ^{(u · t · c)} 19:03, 23 November 2018 (UTC)

@AfroThundr3007730: Thanks!!! So I've got a working proof of concept at {{Infobox chemical}}. Really need some feedback on it. I've got the technical side of the template covered so if you aren't comfortable with editing it, please don't worry. That isn't really where I need help. The help that I need is in finding the holes. What is missing. What is still broken? What needs more work? Etc. If anything jumps out at you as not looking right, please let me know. --Zackmann (^{Talk to me}/_{What I been doing}) 21:25, 23 November 2018 (UTC)

Count me in. Sounds like fun. (And yes, that is semi-ironic, but I seem to have a penchant for painful, rewarding endeavours). ∰Bellezzasolo✡ Discuss 00:27, 24 November 2018 (UTC)

@Bellezzasolo: awesome! Welcome to the party! See the message I left AfroThundr above. Same thing from you would be great. Take a look and give me any thoughts you have? Once we get a few more people to chime in I'll post a message to everyone. --Zackmann (^{Talk to me}/_{What I been doing}) 01:05, 24 November 2018 (UTC)

Conversion Update

So just an update for anyone interested. We have a working replacement for {{Chembox}} at {{Infobox chemical}}. Eagerly looking for feedback on what needs additional work before we roll it out. I've posted in a number of places but have only gotten a few people to chime in.

Improvements

• Reduces WP:OVERLINK & MOS:DUPLINK. Nearly every label in {{Chembox}} is linked including things like Eye Hazard.
• In line with WP:ACCESSIBILITY. There are certainly places that things are showing up much bigger than before, but this follows the requirements of WP:ACCESSIBILITY.
• Fewer templates to maintain. {{Chembox}} has separate templates for nearly every single row in the table, adding up to well over 200 separate templates. WAY more than is necessary.
• Builds on the style, look and feel of {{Infobox drug}}. The Infobox drug template, formally known as {{Drugbox}} was also converted to use {{Infobox}}. This one uses many of the same styles and subtemplates as that.
• Implements much better Check for unknown params. The use of Module:TemplatePar is fine, but it has a much more narrow scope and is not nearly as well documented or maintained as Module:Check for unknown parameters.
• From the editors point of view, works the same. These templates will work exactly the same as the {{Chembox}} series of templates. NO parameters have changed. So apart from having to call {{Infobox chemical}} instead of {{Chembox}}, there is no change to how editors will use the templates. No new parameters & no new syntax. As per the other points made here, there are certainly some stylistic changes to how the template renders, but I want to be clear that for the editor, nothing new except for calling a different template.

Once again, really eager for any and all feedback. Please be sure to look at the testcases as well! --Zackmann (^{Talk to me}/_{What I been doing}) 02:30, 25 November 2018 (UTC)

"before we roll it out". Therefore I have un-marked the existing one as deprecated. If you persist in rolling out a major change that multiple editors have voiced concerns about, you will find yourself blocked for disruption and bad-faith claims of consensus. DMacks (talk) 03:06, 26 November 2018 (UTC)

WOW DMacks. Talk about WP:AGF... Trying my best here. How about you join the discussion instead of just accusing me and threatening me with blocks? --Zackmann (^{Talk to me}/_{What I been doing}) 03:13, 26 November 2018 (UTC)

Disruption is disruption. A major change after others voice concerns (I did and others did as well, even though you explicitly said you were not even interested in receiving such input), and with a major rollout rather than first small-sale testing or even notice that it's happening to the stakeholders is on its face disruptive. WP:CONSENSUS and all that. DMacks (talk) 03:47, 26 November 2018 (UTC)

@Zackmann08: I second DMacks in that: Your behaviour here is disruptive. You are insistent in stuffing this down throats: You start a discussion where many concerns are brought forward, to which you never responded. Then start an RfC with an attempt to shut down any response you don't like. And when that RfC does not go your way, you delete it, and start to convert it yourself. Then you comment, but again do not address cncerns, you go on and mark it as deprecated, and subsequently for deletion withour informing major contributors and the wikiprojects, let alone properly testing it. That behaviour is disruptive. --Dirk Beetstra ^{T C} 03:55, 26 November 2018 (UTC)

@Beetstra:[6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18] and the list goes on. I reached out to you both individually asking for your concerns. Instead, you accused me of stuffing something down your throats. I have reverted the deprecation notice. I admit that was preemptive. Now, I have asked for concerns. Instead of just accusing me of being disruptive, can you provide some feedback on the template? Have you even looked at it? --Zackmann (^{Talk to me}/_{What I been doing}) 03:57, 26 November 2018 (UTC)

@Zackmann08: no, I did not have time with you leaving notices over black Friday/Thanksgiving weekend and pushing for deprecation and even deletion. Can you see how we feel you are stuffing this down our throat: First you do not respond to first concerns, then you put up an RfC where you pre-emptively disqualify any answer you don't like (and then delete it), and now you leave notices over the weekend, expecting editors to respond within 24 hours and already put it up for deletion. And you conveniently leave out the initial discussion and RfC from above list. I am sorry, a spade ISa spade: What you have done here is disruptive (even if possibly well-intended) (and especially since it seems that your TfD is in response to the removal of the deprecation, which appears very pointy). --Dirk Beetstra ^{T C} 04:17, 26 November 2018 (UTC)

(edit conflict) @Beetstra and DMacks: ok look. Clearly I made a few missteps in this process. Let me apologize for being hasty. Let me also apologize for ANY appearance or implication that I was not open to feedback. There is absolutely no intention to stuff this down anyone's throat. From my point of view, I tried my best to notify people and only removed an RfC when multiple people said the RfC was simply disruptive. I was not trying to hide the comments, I just got frustrated being called an armchair commentator, etc. I don't think it is helpful to go back over past actions. If you want to then by all means you can bring up the mistakes I've made and we can fight over whether I did this properly or not. Etc. Etc. OR, we can work together? I think that the new template I have created will meet the needs of all those interested. That being said, I'm sure there are minor things that I have not thought of. That is why I have asked for feedback from you and other experts in the Chemistry project. There are about 50 or so chemical pages that I manually switched over to use the new template. This were part of the testing process. I scrutinized the before and after and could not find any differences that weren't necessary per WP:ACCESS. However, I'm happy to personally revert each of those changes if you feel it is necessary.

Regarding the TFD, I think it might be helpful to keep the TFD to initiate the DISCUSSION and attract more attention to the process. However, if you feel it is premature, I will gladly withdraw the nomination. Again, I am sorry if my tactics in the past sent the wrong message. I would like to start fresh and work WITH you. I'm going to take a step back. There is no timetable here and that is something I keep forgetting. I'm a "full steam ahead! This works great LETS DO IT!" Kind of guy. I need to stop and slow down. I hope that both of you, and others, will work with us to finish up this template so that it will work for everyone. I'm going to walk away from the keyboard for the night because I'm frustrated and don't want to type anything else when I'm in a bad mood. But I sincerely hope we can bury the past and work together. I truly value any input you have. --Zackmann (^{Talk to me}/_{What I been doing}) 04:21, 26 November 2018 (UTC)

@Zackmann08: withdraw your TfD, give concerned editors and wikiprojects a 1-3 month time to test and consider, and let someone else pull final triggers. You have upset quite some editors this weekend. Step away from implementation. --Dirk Beetstra ^{T C} 04:27, 26 November 2018 (UTC)

I have withdrawn the TFD. Sorry for the issues that I caused. If anyone has any questions for me, please feel free to ping me. --Zackmann (^{Talk to me}/_{What I been doing}) 05:53, 26 November 2018 (UTC)

Critical point

Why don't we put the critical temperature and pressure in? Eric Kvaalen (talk) 11:19, 10 December 2018 (UTC)

OK. I'll prepare |CriticalTP= in old {{Chembox}}. See /testcases9.

Positioning: propose in section Propserties, following melting point and boilong point.

|CriticalTP= has free input (any input text will show, unedited). That is, the editor is expected to write the desired outcome: values, units, conversions, text separator T-P, reference. Later on we could apply standard formatting/simplified input).

-DePiep (talk) 16:40, 11 December 2018 (UTC)

Eric Kvaalen See /testcases9 (ammonia demo). Could be in section Thermodynamics instead?

I hope you like the single-input here. Allows you to spell out the values (even use {{Convert}} as desired), without having to bother about parameter names & details (as m.p. and b.p. have). Comments? - DePiep (talk) 17:04, 11 December 2018 (UTC)

@DePiep: Looks fine to me. Thanks. Eric Kvaalen (talk) 10:26, 13 December 2018 (UTC)

Template-protected edit request on 14 December 2018

• Please copy/paste all sandbox code into the live template: {{Chembox Properties/sandbox}} → {{Chembox Properties}}. (Note that this is not about main template {{Chembox}}).

Change: adding parameter option |CriticalTP= (critical point temperature and pressure). Test/demo in /testcases9 (first section).

Per request, proposal & consensus: #Critical_point. -DePiep (talk) 16:47, 14 December 2018 (UTC) DePiep (talk) 16:47, 14 December 2018 (UTC)

 Done --Zackmann (^{Talk to me}/_{What I been doing}) 17:12, 14 December 2018 (UTC)

@DePiep: I'll leave it to you to update the documentation. :-) --Zackmann (^{Talk to me}/_{What I been doing}) 17:14, 14 December 2018 (UTC)

Hi Zackmann08. Updating the documentation was not part of my request, so there is no need to "ask" me to do so. And after all, I have been maintaining the whole {{Chembox/doc}} extensively for six years (check, [19]) consistently. I'm fine, and I also want to note that I do not like your jab with the ":-)" at all. (Usually I would thank an editor in this point for taking care. But alas). -DePiep (talk) 22:20, 14 December 2018 (UTC)

@DePiep: oh for god's sake. Are you incapable of assuming good faith?! The smile was meant as a friendly message!!! Why do you choose to assume I'm taking a jab!? All I meant was "hey I updated the template, but I'll let you take care of the documentation"? Jesus man. --Zackmann (^{Talk to me}/_{What I been doing}) 00:03, 15 December 2018 (UTC)

Stop hiding behind "AGF" for each and every dirty dish you serve. Quite simple: there was no need in any way or sense you had to write that after-post. Or was there? - DePiep (talk) 00:16, 15 December 2018 (UTC)

Believe it or not, my only attempt was to be friendly. I'm sorry you chose to take it another way. Please do not contact me again in any way. I will not reply to any of your posts anymore and will refrain from fulfilling edit requests. It is clear my help or attempts at moving forward are neither appreciated or welcomed. --Zackmann (^{Talk to me}/_{What I been doing}) 00:20, 15 December 2018 (UTC)