Pharmacology
This page is within the scope of WikiProject Pharmacology, a collaborative effort to improve the coverage of Pharmacology on Wikipedia. If you would like to participate, please visit the project page, where you can join the discussion and see a list of open tasks.PharmacologyWikipedia:WikiProject PharmacologyTemplate:WikiProject Pharmacologypharmacology

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Archives

WP:DRUGS Archive 1: 6/2004 – 7/2006 WP:DRUGS Archive 2: 8/2006 – 2/2007 WP:PHARM Archive: 1/2007 2007 2008 2009 2010 2011 2012 2013 2014

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I have completely rewritten DLB; might someone check all of my usage of meds, as well as the wikilinks? SandyGeorgia (Talk) 16:29, 8 April 2018 (UTC)[reply]

I'll take a look this weekend – possibly sooner if I have time. Seppi333 (Insert 2¢) 07:02, 10 April 2018 (UTC)[reply]

Pending action. Seppi333 (Insert 2¢) 07:24, 17 April 2018 (UTC)[reply]

 Done. Excluding one typo that I fixed, nothing seemed amiss. Seppi333 (Insert 2¢) 12:55, 17 April 2018 (UTC)[reply]

Thanks (that was quite a typo ... by me!) SandyGeorgia (Talk) 13:00, 17 April 2018 (UTC)[reply]

As a suggestion, that section – in addition to other very long level 3 sections in the article – would look less congested if level 4 section headers and {{TOC limit|3}} were used instead of bold article text to separate material on different subtopics (e.g., medications for different symptoms clusters). Seppi333 (Insert 2¢) 13:04, 17 April 2018 (UTC)[reply]

An article that you have been involved in editing—Vitamin B3—has been proposed for merging with another article. If you are interested, please participate in the merger discussion. Thank you. SusanLesch (talk) 14:22, 30 April 2018 (UTC)[reply]

Per the policies outlined in this page, I have taken the liberty of updating the participant list. However, after bringing up the topic with Beetstra (as part of an activity update), Beetstra noted that "this was started years ago, and has been totally unmaintained." Before I proceed further with maintaining an old policy, I wanted to get an idea of what the other members of the project thought! Do you see a benefit to updating the list and posting on inactive user's talk pages? If we are to update them, how should we do it? Should the definitions for active/inactive be changed, or eliminated altogether? The template I've used is the following:

==[[Wikipedia:WikiProject Pharmacology|WikiProject Pharmacology]] User Activity Update==

Hi there! I've noticed that you haven't been active on WikiProject Pharmacology. Per our policies, your status has been moved from Active to Inactive, which you can view here. Don't be discouraged, though--we'd love to see you come back and contribute to the project! Let me know if you need any help! ~~~~

A possible pro to maintaining the old standard includes that it may help otherwise inactive members remember that our project exists, and perhaps spur them to make a contribution to a WikiProject Pharmacology article. On the other hand, as Beetstra pointed out on their talk page, it may be discouraging to editors to see their status change from active to inactive, possibly having the opposite of the intended effect.

Let me know what your thoughts are! (: ―Biochemistry🙴❤ 03:21, 1 May 2018 (UTC)[reply]

I have yet to see a discussion that initiated that ‘policy’. —Dirk Beetstra ^{T C} 03:57, 1 May 2018 (UTC)[reply]

Support the implementation of the existing policy, clearly listed above the participants list, and think that adding a notice to their talk pages is helpful. Such is likely to encourage some people to start contributing to the project again. Perhaps add "If you plan to contribute, please return your name to the active list." (or similar) Klbrain (talk) 12:04, 1 May 2018 (UTC)[reply]

@Klbrain: I think that's a good suggestion!―Biochemistry🙴❤ 19:12, 1 May 2018 (UTC)[reply]

@Beetstra: That's a fair question; I think historical context is worth looking at too. I did a little digging, and the earliest mention I can find is a post by Skittleys (that you can find here), whose intention it was to "upgrade the project" by creating the activity differences, and maintaining them. The suggestion appeared to have passed without much discussion of the specifics at the time. I hope that helps!―Biochemistry🙴❤ 19:12, 1 May 2018 (UTC)[reply]

@Biochemistry&Love: that is indeed the post I was looking for. Not much more than a fleeting mention though. —Dirk Beetstra ^{T C} 19:28, 1 May 2018 (UTC)[reply]

Oppose current wording and methods but no opinion on the whole idea. Why not retitle the categories "participants" and "highly active participants", with a "thank you for being so active" message upon promotion (reward) and just a "we notice you have not been highly active lately" (rather than feeling like demotion/exclusion just not the positive). Compare to WP:MED's annual roundup of "top contributors" notices. DMacks (talk) 12:54, 1 May 2018 (UTC)[reply]

I also oppose the current criteria as giving more leeway to those who wander away from WP as a whole for many months still being "active" whereas those who are highly active on the site have a higher activity requirement in the field. I think either one is highly active in the field or one isn't. Do we have data about editor retention for how long we (Wikiproject, or WP as a whole) waits before trying to lure back? DMacks (talk) 12:59, 1 May 2018 (UTC)[reply]

@DMacks: Hmm. I suppose that proposal would change the emphasis to providing positive feedback (carrot) as opposed to negative feedback (stick). What about doing both--i.e., adding a third category for "high active participants?"

My guess behind the intention there was that retention efforts should be especially focused on high-output users; i.e., users that are already spending a lot of time on Wikipedia. After all, if you can retain a high-output editor, you get more bang for the buck. I'm not aware of any data on how long other projects wait before making efforts to re-engage "inactive" users, or if other cut-offs or categorizations exist.―Biochemistry🙴❤ 19:12, 1 May 2018 (UTC)[reply]

I second DMacks here. As I said elsewhere, I can see advantages in moving generally inactive users, but this stick method is certainly not encouraging .. moreover, this list is not maintained for 9 odd years, and now you ‘demote’ active editors who did not edit in the field (by whatever measure) for a month. —Dirk Beetstra ^{T C} 19:28, 1 May 2018 (UTC)[reply]

I agree with other editors that a carrot, not stick, approach is the way to go. But frankly, nobody should care about making sure that active lists are purged of anyone who is inactive (I'm saying that in general, not just here). There are things – like articles! – on Wikipedia that need to be kept current, but this isn't one of them. The greatest good would come from simply encouraging more editors to contribute actively. --Tryptofish (talk) 20:48, 1 May 2018 (UTC)[reply]

@Beetstra: Just to be clear, the "demotion" from active to inactive is 6 months for no contributions, 3 months if reasonably active, and 1 month if extremely active (>1000 edits). You don't think that there are some users that may be motivated by the "stick" method, as Klbrain commented? I.e., the internal dialogue of, "I want to be an active contributor, and my status will move to inactive if I don't do something. Therefore, I will make a contribution." It seems reasonable to me, but that's only my personal viewpoint.

@Tryptofish: I don't think the point ever was for the sake of the list itself; rather, the list was a means to an ends of providing motivation for the purposes of editor retention. Do you think we should remove the "active" and "inactive" categories entirely, and simply have a list of members? DMacks suggested the category of "highly active participants," with the removal of the "inactive" category. ―Biochemistry🙴❤ 01:28, 2 May 2018 (UTC)[reply]

Actually, I don't have a strong opinion about that, either way. Just that the approach should be "carrot". Probably, that means doing away with "inactive" in favor of a more positive name, but what the name or location should be doesn't matter to me. --Tryptofish (talk) 01:48, 2 May 2018 (UTC)[reply]

@Tryptofish: That seems to be the position of DMacks as well (correct me if I'm wrong). I'm curious: why do you (or others) think that the "stick" method of having an "inactive" categorization isn't a good strategy for promoting retention? Beetstra thought it may be discouraging. Notably, I believe that WP:MED also has an inactive list (albeit, managed by a bot), but does not post on talk pages. In contrast, WP:CHEM has a list without active/inactive categorization. Perhaps we could gain some insight on what WP:PHARM should do by asking members of these groups for their input, on how their participant lists are working out for them. Thoughts on that as well?―Biochemistry🙴❤ 18:10, 2 May 2018 (UTC)[reply]

I think that if an editor previously put themselves on the active list, having someone else move them to inactive is sort of like saying that we don't think you're doing enough any more. That sounds negative. But I'm aware that active/inactive is very common at many WikiProjects. And it's an incredibly unimportant detail for me. I don't think it's worth doing research at other projects, but if it's you and not me doing it, that's up to you. I think the best place to ask about it would actually be at Wikipedia:WikiProject Council. --Tryptofish (talk) 18:18, 2 May 2018 (UTC)[reply]

FYI, WP:MED does what I think is about the max one should do - move editors who have not edited AT ALL for some time (they have a month). Anything else says ‘you are not doing enough for us). (Did someone now locate a proper discussion regarding these rules?). —Dirk Beetstra ^{T C} 18:53, 2 May 2018 (UTC)[reply]

WP:MED posts a thanks/note to editors who are highly active within the past year, unrelated to whether they sign onto the project. A "pure carrot". WP:PHARM could tighten the wording of its carrot (or reduce the pain of the stick) by identifying the list as "highly active within the past month" (or "active within the past 3 months") to clarify what the scope is (goes back to my dislike of differential thresholds). DMacks (talk) 06:09, 3 May 2018 (UTC)[reply]

@Tryptofish: It does sound "negative" to suggest that someone is being inactive, but isn't there an implied sense of duty to be counted as an active member of a group? At some point, we have to call a spade a spade: is anyone arguing that the current inactivity criteria doesn't actually represent inactivity, or just that it can be demotivational to be told that you're inactive? Thank you for the suggestion of reaching out to the Wikipedia:WikiProject Council; I've started a discussion here. ―Biochemistry🙴❤ 23:56, 3 May 2018 (UTC)[reply]

Since you asked me, no. I think we are all volunteers here, and nobody has an obligation to do more than what they feel like doing. I think we should always be appreciative of whatever we can get. --Tryptofish (talk) 00:26, 4 May 2018 (UTC)[reply]

I don't disagree whatsoever--we should be appreciative. I don't think that means that we shouldn't encourage people to contribute, however. And if everyone is counted as "active," then activity loses its utility. A participant list that doesn't list actual participants is meaningless. If I volunteer once with the Red Cross, and never again, am I still an "active participant?" Is there no utility to having a list of active and inactive participants of a project?―Biochemistry🙴❤ 00:46, 4 May 2018 (UTC)[reply]

That raises the underlying question "what is the actual use of publicly listing those that are active?". DMacks (talk) 15:02, 5 May 2018 (UTC)[reply]

Good question. In my opinion, it ranks very, very low among the ways that Wikipedia does anything to be of service to our readers. Kind of not even worth having as much discussion as we are having here. But I think the one good that it does is to provide a bit of acknowledgement among editors for those who have been interested in a project, along with providing a way for editors to communicate with one another within the project. But I continue to feel strongly that it should have nothing to do with giving thumbs up or thumbs down on any one editor's contributions. If anyone were to tell me something like "In my opinion, you need to be making more edits in such-and-such a topic area", my reaction would be "I'm a volunteer, so fuck you!". I try as best as I can to avoid saying divisive things out loud on-wiki, but that is what would go through my mind. --Tryptofish (talk) 15:17, 5 May 2018 (UTC)[reply]

It is also worth considering the utility of listing "inactive" users. Perhaps these are people we can reach out to and remind them about the project, as per my suggestion above. I think that Tryptofish's response to a request for volunteerism is a bit extreme; I mean, when I get calls from blood donation centers, my first thought isn't "fuck you for asking for my help, vampires," even if I know I can't find time to come in at the moment. And, as a result, I don't pretend to be an "active" blood donor if I haven't given in a long while. It just feels extreme to have a powerfully negative, emotional reaction to a simple, kindly-put reminder that the project exists, and I don't understand how it can be offensive to be moved to "inactive" when you're not, well, active. I don't think that the majority of users notified of their inactivity would react that way. Is there really not a kind way to do it? I disagree that this is akin to giving a "thumbs up or thumbs down" to an editor's contributions; rather, we're discussing the frequency of an editor's activity. And, how else (but an editor's activity) should we discuss how active they actually are?

On a related note, I've received a link to a bot-maintained list of "active" participants (defined differently than the current participant page; it is even more stringent than the current "active" criteria, only listing users with 5 or more edits within 30 days!), which you can find here. Is this definition of "activity" preferable to the more lenient guidelines we already have? For people that don't edit at all, the current criteria give 6 months for a user to make an edit (just one!) to still be counted as "active." Even for "reasonably active" users, we allow a 3 month period for a user to make an edit. A every 30 day requirement for "active" status currently only applies to users with over 1,000 edits/month, and is still more lenient by requiring only 1 edit instead of 5.―Biochemistry🙴❤ 23:06, 6 May 2018 (UTC)[reply]

Well, I hope nobody at this project asks for my blood. --Tryptofish (talk) 23:58, 6 May 2018 (UTC)[reply]

Oh, this is awkward.. I'll uhh.. just go ahead and delete this then.. 😅―Biochemistry🙴❤ 18:40, 7 May 2018 (UTC)[reply]

I think that Biochemistry & Love is on the right track with the link to Wikipedia:WikiProject Directory/Description/WikiProject Pharmacology. If you need something that's truly up to date, then that page does it for you. WhatamIdoing (talk) 23:21, 14 May 2018 (UTC)[reply]

Sorry for abandoning this discussion for a while, but how do people feel about simply blanking the current Wikipedia:WikiProject Pharmacology/Participants page, and redirecting to the bot-maintained list located at Wikipedia:WikiProject Directory/Description/WikiProject Pharmacology? Unless we can transform the page into a sort of pure carrot? I don't know how WP:MED identifies highly active users.―Biochemistry🙴❤ 18:27, 10 June 2018 (UTC)[reply]

There are 22 articles at Category:Pharmacology articles needing expert attention. It's been my experience that many pages with this tag (perhaps even most) don't actually need attention from an expert, and especially if it's been tagged for years, the problem may have been solved. Please consider looking through the tagged articles, removing stale/inexplicable tags, and bringing a short list of the ones that need particular attention back to this page. WhatamIdoing (talk) 23:24, 14 May 2018 (UTC)[reply]

Removed a few irrelevant tags. Seppi333 (Insert 2¢) 00:35, 15 May 2018 (UTC)[reply]

@WhatamIdoing: Thank you for bringing this up! In the process of going through some of these articles and removing tags as well. ―Biochemistry🙴❤ 02:02, 15 May 2018 (UTC)[reply]

You all are awesome. Just three and a half hours later, and more than half the articles have already been looked at. WhatamIdoing (talk) 03:00, 15 May 2018 (UTC)[reply]

Just 8 in the category now. I'm amazed. WhatamIdoing (talk) 04:50, 14 June 2018 (UTC)[reply]

Radiopharmaceutical was never tagged for WP:PHARM and a year-old merge request (from List of radiopharmaceuticals, that is tagged) never got any response until I noticed it today and added yet a different option. I'd appreciate others' comments at Talk:Radiopharmaceutical#March 2017 Proposed merge so it can get resolved one way or another (and also whatever assessment/tagging the project feels is appropriate). DMacks (talk) 16:51, 20 May 2018 (UTC)[reply]

I've replied there, and it looks to me to involve a couple of complexities, so it would be helpful if more editors would check on it. --Tryptofish (talk) 19:35, 20 May 2018 (UTC)[reply]

The reason I am contacting you is because there are one or more portals that fall under this subject, and the Portals WikiProject is currently undertaking a major drive to automate portals that may affect them.

Portals are being redesigned.

The new design features are being applied to existing portals.

At present, we are gearing up for a maintenance pass of portals in which the introduction section will be upgraded to no longer need a subpage. In place of static copied and pasted excerpts will be self-updating excerpts displayed through selective transclusion, using the template {{Transclude lead excerpt}}.

The discussion about this can be found here.

Maintainers of specific portals are encouraged to sign up as project members here, noting the portals they maintain, so that those portals are skipped by the maintenance pass. Currently, we are interested in upgrading neglected and abandoned portals. There will be opportunity for maintained portals to opt-in later, or the portal maintainers can handle upgrading (the portals they maintain) personally at any time.

On April 8th, 2018, an RfC ("Request for comment") proposal was made to eliminate all portals and the portal namespace. On April 17th, the Portals WikiProject was rebooted to handle the revitalization of the portal system. On May 12th, the RfC was closed with the result to keep portals, by a margin of about 2 to 1 in favor of keeping portals.

There's an article in the current edition of the Signpost interviewing project members about the RfC and the Portals WikiProject.

Since the reboot, the Portals WikiProject has been busy building tools and components to upgrade portals.

So far, 84 editors have joined.

If you would like to keep abreast of what is happening with portals, see the newsletter archive.

If you have any questions about what is happening with portals or the Portals WikiProject, please post them on the WikiProject's talk page.

Thank you.    — The Transhumanist   11:00, 31 May 2018 (UTC)[reply]

Hi, I am a current student in the pharmacy field, and I am currently researching the completeness of drug Wikipedia articles. I stumbled upon your project page and was wondering how long this group has been going. Also the credentials of your main editors. I am new to Wikipedia editing and am trying to get a general idea of what the standards of your group are. Thank you in advance. — Preceding unsigned comment added by RosalindPK (talk • contribs) 18:00, 8 June 2018 (UTC)[reply]

Hello, and welcome to Wikipedia! As for credentials and standards, anyone is welcome to edit Wikipedia constructively. You should free to WP:BEBOLD. I suggest getting familiar with WP:PHARMMOS and WP:MEDRS as a way to get familiar with writing standards. And feel free to ask questions! --Tryptofish (talk) 18:07, 8 June 2018 (UTC)[reply]

@RosalindPK: As Tryptofish said, the only "standards" are those that apply to the project as a whole. The two standards cited are must-reads, and will definitely make contributing easier. If you have any questions, feel free to drop by here or on my talk page. Welcome to Wikipedia! ―Biochemistry🙴❤ 03:39, 10 June 2018 (UTC)[reply]

Intend this with the upmost respect, but realize it might be impossible to say without sounding a bit rude, I really don't mean it to be. I think the question above needs to be re-addressed, because the question was what the credentials of the main editors of this group are, not whether or not one needs credentials to edit Wikipedia. All due respect, but that question remains unanswered. I point this out because I've started to notice a fairly substantial number of errors on pages related to pharmacology, and because there appear to be restrictions on who can edit that content. How is consideration given as to the best way to balance good quality information, against obstructing corrections where there are errors on these articles? Cheers CanisLupisArctus (talk) 00:31, 10 June 2018 (UTC)[reply]

I don't think we've ever been surveyed. That said, the number of people who edit pharmacology articles on Wikipedia is FAR larger than the number of people in this WikiProject. Seppi333 (Insert 2¢) 00:36, 10 June 2018 (UTC)[reply]

@CanisLupisArctus: No worries, that's a fair question to ask. Simply put, there are no "credentials" required; anyone is free to edit these articles. If you notice errors, feel free to be WP:BOLD and fix them yourself, point them out on the talk page, or ask for assistance here. The "quality" of information should never be in much dispute, as long as reliable sources are being used, but we employ consensus when disagreements occur. ―Biochemistry🙴❤ 03:39, 10 June 2018 (UTC)[reply]

It occurs to me to add another point. The way that Wikipedia is set up, the concept of editors needing to have "credentials" does not apply at all. A big part of this is that everyone has the right to edit anonymously, and that is something that the community cares about a lot. As far as I'm concerned, if a Nobel Laureate makes an error in an edit, I'm going to fix it, and if a young child makes a good edit, I'm going to support it. --Tryptofish (talk) 17:45, 10 June 2018 (UTC)[reply]

The Zaleplon article states "Zaleplon, like zolpidem, zopiclone, or eszopiclone, are all specific agonists at the benzodiazepine GABAA α1 sub-receptor site.". There is no citation, and I am uncertain about use of the term 'specific agonist'. Can someone please educate me as to the use of this term? At first I presumed this was meant to say 'selective agonist', as I haven't often heard the former term being used. But upon searching I found an article published in Nature that uses the term in its title, and I can't imagine it's very likely that the editors of Nature wouldn't have corrected a terminological error in a publications title. Either way, I am fairly certain that the content of the statement is not correct, in that Zopiclone, for example, acts indiscriminately, as a full agonist, at four of the five alpha subunits of the GABAA receptor - https://www.drugbank.ca/drugs/DB01198 — Preceding unsigned comment added by CanisLupisArctus (talk • contribs) 00:27, 10 June 2018 (UTC)[reply]

@CanisLupisArctus: Thank you for bringing up your concern about the zaleplon article. To answer your question, my guess is that the writer meant to convey that the agonism is "selective," as in "affecting some things and not others," of which the term "specific" (meaning "belonging or relating uniquely to a particular subject") is an improper approximation of. I've corrected the area you've mentioned, and made a few more edits to the article, which could still use a lot of work! For the future, when you have a concern about an article, you can bring it up on the article's talk page; for the zaleplon article, that is here.―Biochemistry🙴❤ 04:08, 10 June 2018 (UTC)[reply]

Thanks, not sure why it wasn't working earlier I had assumed only some could edit the talk page. My mistake. Cheers! CanisLupisArctus (talk) 01:54, 19 June 2018 (UTC)[reply]

User:Natureium has very kindly taken up my request to write about Drug titration. It looks like it's easy to find sources about drug titration in specific instances, but information about the general concept seems to be harder to identify. Can anyone help out with a good source or two? WhatamIdoing (talk) 04:52, 14 June 2018 (UTC)[reply]

Found at least one. Boghog (talk) 09:28, 14 June 2018 (UTC)[reply]

Thanks! Natureium (talk) 13:59, 14 June 2018 (UTC)[reply]

FYI: I just extended the range of acceptable inputs for the "class" parameter in {{WikiProject Pharmacology}} to include category-, disambig-, draft-, file-, portal-, project-, template-, and redirect-class ratings for pharmacology-related pages and created the corresponding categories. So, in a nutshell, our project's article/page rating template now includes categorization for those subject page types. Seppi333 (Insert 2¢) 22:29, 14 June 2018 (UTC)[reply]

FA	A	GA	B	C	Start	Stub	FL	List	Category	Disambig	Draft	File	Portal	Project	Redirect	Template	NA	???	Total
11	0	50	671	1,927	5,219	7,238	1	513	1,459	14	38	47	0	23	978	404	16	286	18,895

I've noticed that there don't appear to be any pages pertaining to pharmacy law in US states (or at the national level). There's a lot of work on gun laws and LGBT rights by state, and I'm not sure if this would be better suited to the purview of Wikipedia:Law, but I was wondering if anyone wanted to collaborate on anything.―Biochemistry🙴❤ 22:45, 19 June 2018 (UTC)[reply]

@Biochemistry&Love: How close is Regulation of therapeutic goods to what you want? Blue Rasberry (talk) 00:33, 20 June 2018 (UTC)[reply]

Thank you for the reply! I think that's a great page, but I'm thinking about pages more narrow in scope, along the lines of Pharmacy laws in Michigan, Pharmacy laws in Indiana, etc. (analogous to Gun laws in Michigan, Gun laws in New York, Gun laws in New Mexico, etc.). Something that reflects the nature of pharmacy practice in these states, and eventually abroad.―Biochemistry🙴❤ 02:04, 20 June 2018 (UTC)[reply]

There are frequently pages for the relevant legislative acts; some of them are listed at Drug control law and elsewhere. Klbrain (talk) 21:52, 20 June 2018 (UTC)[reply]

All good things! However, I don't think these pages reflect pharmacy practice.―Biochemistry🙴❤ 00:22, 21 June 2018 (UTC)[reply]

@Biochemistry&Love: I think this is overly ambitious. I tried to make User:Bluerasberry/Healthcare in Washington (state) a few years ago but felt stumped for sources. With some other states in Category:Healthcare in the United States by state I was more successful. Blue Rasberry (talk) 18:44, 21 June 2018 (UTC)[reply]

For US the pattern that I see is some but not all states have "healthcare" articles. More states have "list of hospital" articles. Some states have "department of health" articles. I am not opposed to pharmacy law articles but I have my doubts that these can stand when the regional "healthcare" articles are so shabby. The most developed regional healthcare articles are Category:Cannabis in the United States by state. Blue Rasberry (talk) 18:43, 21 June 2018 (UTC)[reply]

Moved from User talk:Seppi333

 – Tom (LT) (talk) 18:18, 3 July 2018 (UTC)

Hey Seppi333. Wondering if I could pick your brain. I often use WP as revision and for my work as I'm sure many people do. I find many of our articles (e.g. Beta-2 adrenergic receptor, which I'm looking at now) very difficult to read and lacking key information which (I feel at least) could be included in the infobox - e.g. where is that thing, what does that thing do, what makes that thing). I don't want to reinvent the wheel discussion wise so I thought I'd ask if any of those discussions have happened before, and what do you think about some sort of approach to making these articles somewhat more readable? Looking forward to your response, --Tom (LT) (talk) 23:24, 30 June 2018 (UTC)[reply]

@Tom (LT): Hmm. I would probably ask at WT:PHARM about this since I don't remember this being mentioned before (NB: it'd be worth mentioning that WT:PHARM discussion and linking to it at WT:MCB). A typical article on a receptor protein uses Template:Infobox gene (e.g., TAAR1 and DRD1), but a modified infobox for a receptor analogous to Template:Infobox neurotransmitter might be merited for use as a 2nd contextual infobox in articles on G protein-coupled receptors (e.g., beta-adrenoceptors). As for making the Beta-2 adrenergic receptor article more readable, the structure/mechanism section are both necessarily technical, but I suppose a signal transduction diagram in the mechanism section might help. The function section should probably be converted mostly to prose.

I'm not sure which part you were referring to specifically, but examples of how I typically cover classes of GPCRs and specific GPCRs in articles on those topics are Trace amine-associated receptor and TAAR1; if you think those are adequate, I suppose we could create a discussion about what information to cover on receptor proteins as well as how to format it in the corresponding style guideline (MOS:MCB). Otherwise, it's probably worth requesting more input from others about what should be covered in articles on GPCRs as well as how it should be sectioned/formatted. Seppi333 (Insert 2¢) 22:32, 2 July 2018 (UTC)[reply]

A bit more information may be found under the collapsed Gene ontology section of the {{Infobox_gene}} template including the Molecular function (more specifically the molecular mechanism of action, or more simply what it does), the Cellular component (where it is located within the cell), and the Biological process (cellular mode of action, the end result of what it does). All proteins are basically are made the same way (DNA → mRNA → protein) but the details may differ (e.g., post-translational modification). The data in these infoboxes was taken from databases and much of it may be difficult for most readers to digest. Perhaps we should add some fields for human generated descriptions. Boghog (talk) 10:41, 3 July 2018 (UTC)[reply]

It doesn't seem to me that infobox gene is appropriate for neurotransmitter receptors, because so many of them consist of multiple subunit proteins. I think perhaps an appropriate infobox would contain at minimum a list of agonists, antagonists, mechanism of action, and component proteins. Looie496 (talk) 14:04, 3 July 2018 (UTC)[reply]

Specifically discussing infoboxes (which are only one small aspect of readability), I agree with Looie. We do have {{Infobox protein}}, which is significantly more appropriate than one about genes. However, I think it would be an even better idea to create {{Infobox receptor}}, with a more pharmacological (ligand-oriented) focus. --Tryptofish (talk) 19:33, 3 July 2018 (UTC)[reply]

What is misleading about these two infoboxes are the names. Both {{infobox gene}} and {{infobox protein}} contain information about the gene and the protein encoded by that gene. Ditto for the articles transcluding these templates. Every single field that is contained in {{infobox protein}} is also contained within {{infobox gene}}. It makes no sense to have separate articles or infoboxes about the gene or protein. As a practical matter, if a receptor is composed of two or more subunits encoded by different genes (e.g., Interleukin-7 receptor), it is better to use {{infobox protein}} since including more than one {{infobox gene}} template in the same article would overwhelm the article. Boghog (talk) 20:44, 3 July 2018 (UTC)[reply]

If we do create {{Infobox receptor}}, I believe it should not duplicate information already included in {{infobox gene}}. Boghog (talk) 20:57, 3 July 2018 (UTC)[reply]

The old {{GNF Protein box}} that preceded {{Infobox gene}} contained a field for the IUPHAR ID which provided link to the IUPHAR database of receptors/ion channels. I will see if I can get this working again. Boghog (talk) 06:38, 4 July 2018 (UTC)[reply]

It is my opinion that the gene infobox needs to be more readable. See for example (Sex hormone-binding globulin). Almost two vertical pages of identifiers are contained within the infobox. Yet barely any information useful to the lay reader such as - what does the globulin do? where is it produced? what species is it present in? Our templates should serve our readers (most of which will be lay readers, not technically conversant) and I think our current set could be improved in this regard.--Tom (LT) (talk) 09:35, 4 July 2018 (UTC)[reply]

Also, as a reader who is somewhat conversant in biology, I have to say it is confusing to access articles about proteins and have an infobox that is primarily describing a gene. I can see that some protein articles also cover the gene, however the infobox should reflect the primary topic of the article (first sentence: "steroid-binding globulin (SSBG) is a glycoprotein ").--Tom (LT) (talk) 09:39, 4 July 2018 (UTC)[reply]

To reiterate, {{infobox gene}} is NOT primarily about genes. It is about both the protein and the gene. The first identifiers in the infobox are about crystal structures of the protein, not of the gene. If a graphic is included in the infobox, it is most commonly a protein crystal structure that is displayed at the top of the infobox (see for example the infobox in insulin and now also sex hormone-binding globulin). In addition, there are several protein specific links such as UniProt and RefSeq (protein). Even the links to external gene databases have significant information about the protein.

Likewise the articles that transcribe these templates are not solely about the protein. They also contain information about the gene (see WP:MCBMOS). Since the two topics are so interrelated, it makes no sense to split these articles in two. Hence it is appropriate to have a single infobox that contains information both about the protein and the gene and {{infobox gene}} fulfills that requirement. In cases where we have had separate gene and protein articles, these have been merged. Finally I agree that the layout could be improved, but that is a separate issue. Boghog (talk) 12:27, 4 July 2018 (UTC)[reply]

Concerning the lead sentence of Gene Wiki articles, as discussed here and here, we have tried to make clear that the scope of these articles encompasses both the protein and gene encoding that protein. Furthermore these articles are not only about the human gene/protein, but also orthologs that exist in other species. The wording that was reached through consensus is perhaps a little awkward, but it is both accurate and concise:

• <recommended UniProt name> is a protein that in humans is encoded by the <approved HUGO gene symbol> gene.

The "that" in the above sentence is non-limiting implying that the protein (and gene) exists in other species besides human. Boghog (talk) 13:54, 4 July 2018 (UTC)[reply]

In order to enable the external IUPHAR target database links, a new wikidata property for IUPHAR Target IDs must be created. Please comment here if you have an opinion. Boghog (talk) 11:13, 5 July 2018 (UTC)[reply]

I respect the consensus that's been established here - it makes sense to have to have most genes and proteins covered in the same article (although I note that you are linking me to an essay). The phrasing of the lead and structure of the articles implies the articles are primarily about (1) the protein, and (2) the human part of it. Do you think the infoboxes could be made more readable? I am hoping the answer is yes. Some thoughts as to how are - (1) more human readable fields (2) for protein articles, more prominence about the protein (3) deprecating some infobox information to as appropriate (a) an authority control or (b) an additional resources template stored in 'see also'. Thoughts or ideas from you and other editors? I think we all agree WP is a work in progress and therefore there is no harm and the potential to improve many of our articles here. Respectfully, --Tom (LT) (talk) 17:57, 5 July 2018 (UTC)[reply]

I should add, I am fully supportive of inclusion and linking to Wikidata items. It is more of where and how data are appropriately displayed. For comparison, we have recently gone through a similar process at WP:ANAT and it seems WP:MED is making a transition at the moment. --Tom (LT) (talk) 17:59, 5 July 2018 (UTC)[reply]

Thanks for your thoughtful replies. I am all in favor of making these templates more readable. In response to your suggestions:

1. more human readable fields – We could create fields such as |function=, |tissue distribution=, |subcellular distribution=, |copy number=, |synthesis=, |metabolism=, |half-life=, and |post-translational modification=. Please keep in mind we now have over 10,000 distinct Gene Wiki pages. The question is how to populate these new fields. One possibility is to use the data in the Gene ontology, but would only populate some of the fields and probably would have to be reviewed by human editors and hence would involve an enormous amount of work. Of course, we could initially concentrate on the most accessed pages first. Please also note that the title of the Gene ontology section is misleading. It actually has more to do with the protein than the gene. The reason for the name is that molecular biologists and bioinformaticians tend to use gene and protein names interchangeably. (See also Avoid Gene Products)
2. more prominence about the protein – All of the above proposed fields deal with the protein and we can place these near the beginning of the infobox. And as pointed out above, the Gene ontology section is actually more about the protein than the gene. Perhaps this section should be renamed to more accurate reflect what it contains. Finally the RNA expression pattern should probably be collapsed.
3. moving details to an authority control – not sure that this is really needed, especially if these links are moved toward the end of the infobox. Boghog (talk) 19:20, 5 July 2018 (UTC)[reply]

I couldn't agree more with Tom (LT). Many of the protein/gene articles probably get minimal traffic outside the professional biology community, but even relatively popular pages like BRCA1 have infoboxes that are populated almost entirely with material that is likely incomprehensible to the overwhelming majority of readers. And the GO functions are included in that infobox but again likely give no information to the average reader. I'd support moving much of the information currently in the gene/protein infoboxes into a template near the bottom as is currently done with taxonomic identifiers by the Taxonbar. Perhaps more prominently shown could be some human-readable fields as Boghog suggests above. I particulary like his idea of a "function" parameter. Ajpolino (talk) 22:27, 5 July 2018 (UTC)[reply]

Re: #1 in Boghog’s list - that’s more-or-less what I was thinking when I suggested creating a supplemental receptor infobox. I think other useful/relevant fields for that infobox are: |primary endogenous agonists=, |signal transduction= or |transduction mechanism=, and |constitutively active=. If it’s possible to source the relevant data from IUPHAR to wikidata, then we might be able to use their database to populate the fields for the primary endogenous agonists and signal transduction. Not sure where to source data on constitutive activity; that might need to be added manually and coded as a parameter that accepts a binary/{{YesNo}} input. Seppi333 (Insert 2¢) 02:31, 6 July 2018 (UTC)[reply]

Just to put things in perspective, only about 500 of the 11,000 proteins in the Gene Wiki act as receptors. Also it is important to realize that molecular biology is complicated, really complicated. A single protein may have multiple functions that will be difficult to capture with in a single set of parameters. In addition, many proteins have unknown function, but the gene has clear disease linkage. At one point, automatic display of disease associations based on data from an external database was enabled, but the data wasn't considered reliable enough and the display was surpressed (see this discussion). That will be a problem with other types of bot generated descriptions as well. The only way to do this right is manually and that is an enormous amount of work for 11,000 pages. Boghog (talk) 04:41, 6 July 2018 (UTC)[reply]

I imagine that a receptor infobox like this is really only useful and easy to populate for articles on well-known GPCRs, as opposed to things like receptor tyrosine kinases and ligand-gated ion channels (NB: I realize there are a number of "well-known" receptors that belong to both of these classes, but it'd be hard to populate the "function" field for many of these). Given the page traffic on notable GPCRs (most of which are these GPCRs) and the fact that the original issue pertained to a GPCR, shouldn't we just limit the scope of the problem to the underlying issue and create an {{Infobox GPCR}}? The number of human GPCRs, according to GPCR#Classification, is ~750, several hundreds of which are olfactory GPCRs. If we ignore all purely olfactory GPCRs and orphan GPCRs, then I don't think it would be too much work to manually add and at least partially expand the infobox in the corresponding articles. The number of articles involved is only a couple hundred. Seppi333 (Insert 2¢) 02:33, 8 July 2018 (UTC)[reply]

I agree that we should start with well characterized proteins. On the other hand, I don't think {{G protein-coupled receptors}} are necessarily any more or less understood than {{Tyrosine kinases}} or {{Ligand-gated ion channels}}. One really simple thing that could be done to improve readability is to collapse (1) Gene location (Human) (IMHO, this is just eye candy that takes up a lot of space) and (2) RNA expression pattern and uncollapse (3) Gene ontology. This works pretty well in cases where Gene ontology is concise (e.g., TAAR1) and less well where it is verbose (e.g., Beta-2 adrenergic receptor). If we could just figure out a way to restrict Gene ontology to the main or most important functions, this would go a long way to solve the problem. Boghog (talk) 05:31, 8 July 2018 (UTC)[reply]

GO Slim and Subset Guide is a possibility. Especailly relevant might be the Chembl Drug Target slim. Boghog (talk) 05:43, 8 July 2018 (UTC)[reply]

Restricting the level might also help. Boghog (talk) 05:57, 8 July 2018 (UTC)[reply]

Or maybe I am being naive. A verbose gene ontology is just a reflection of the fact that a single gene/protein can have many functions. Boghog (talk) 06:07, 8 July 2018 (UTC)[reply]

Using the Gene Ontology section in Beta-2 adrenergic receptor as an example, if we were to flag in wikidata (adrenoceptor beta 2 (Q287961)) the following subset for display in the infobox:

We would then have a concise description of the most important functions and properties of this receptor. This would still require a lot of manual work to implement for the whole Gene Wiki, but it would be much less work than creating descriptions from scratch. Boghog (talk) 07:48, 8 July 2018 (UTC)[reply]

Hmm. Yeah, that seems like it would work for most GPCRs. The set of GO terms in beta-2 adrenergic receptor's infobox definitely looks to be comprehensive. After checking about 10 other GPCR articles (including one not-so-well characterized one: orexin receptor 1), the lists of GO terms are accurate and at least moderately comprehensive descriptors for the GPCRs as well. There was one exception; given the amount of research on it, the tiny list of GO terms for TAAR1 saddens me. TAARs don't seem to get much attention. In any event, I'll look at other GPCR pages tomorrow since I only looked at a tiny fraction of them tonight.

What do others think? Seppi333 (Insert 2¢) 09:33, 8 July 2018 (UTC)[reply]

There appears a mechanism already in place to rank wikidata (see d:HELP:Ranking). Currently all the Gene Ontology data appears to have a "normal" rank. For Gene Ontology data that we would like to highlight in the infobox, we can change the rank from "normal" to "preferred". It should then be possible to modify the infobox template code to display preferred Gene Ontology data (like the above example) in a new uncollapsed section near the top of the infobox. Perhaps we could call this section "Key Facts". For completeness, the collapsed section containing all the Ontogeny data would be retained.

It will however be rather tedious to use the GUI to change the rankings of a large number of data records. Perhaps we could get a bot to do this. Boghog (talk) 13:25, 8 July 2018 (UTC)[reply]

I’ve expanded and tinkered with several wikidata entries, so I’m already familiar with the ranking feature (although I still have no clue what purpose it serves, so perhaps I should read that link).

That said, how would we code the bot in a manner that would enable it to correctly determine what a receptor’s relevant/notable functions, processes, and cellular distributions are? Unless there’s something I’m missing (e.g., there’s already data on “important” GO terms for most GPCRs somewhere or there’s ranking data for each receptor’s GO terms), that sounds like it’d require an excessive amount of manual work (i.e., data entry if the script references a data file or coding if the relevant terms for each receptor are specified in the bot’s script) for whoever writes the bot script. I’d propose the alternative option of using a machine learning model to do this and having a group of editors manually correct any mistakes if I knew an editor with ML modeling expertise, but unfortunately I don’t. That would entail much less work overall and spread it over multiple individals though. Seppi333 (Insert 2¢) 18:25, 8 July 2018 (UTC)[reply]

That's actually not what I am proposing. What I am proposing is to download Gene Ontogeny data, one protein family at a time, manually go through the list to select "preferred" data, and then have the bot change the rank for the selected data. I know, this is a lot of work, but how else would one do this? I don't think AI is up to the task. There will be a lot of similarities in promoted data within a family, so processing the data family wise should speed up the process considerably. Boghog (talk) 20:18, 8 July 2018 (UTC)[reply]

@Boghog I'd also be happy to help with this. --Tom (LT) (talk) 14:04, 13 July 2018 (UTC)[reply]

Great! I appreciate that. It will take me a few days collect and organize the data. As soon as that is done, we can divide up the work to identify preferred data by protein family. Boghog (talk) 16:55, 13 July 2018 (UTC)[reply]

Break inserted here to keep track of subtopics --Tom (LT) (talk) 14:04, 13 July 2018 (UTC)[reply]

I think there is something very important that is not being addressed in this discussion (some of which I find tl;dr, admittedly). A receptor infobox should not be treated as something in molecular biology, as the two of you appear to be doing. If that were the case, we could just as well stick with the existing templates. What is really needed is the pharmacology: agonists, antagonists, modulators, and their pharmacologic/medical classifications. --Tryptofish (talk) 18:57, 8 July 2018 (UTC)[reply]

We clearly have two (or more) audiences here. Where this discussion started was a request to improve the readability of the gene infobox. This would include all proteins, not just receptors. I am also in the process of restoring the IUPHAR target links (see for example 5-HT_1A receptor) so that the gene infobox contains at least one receptor specific link. The Gene Ontogeny section would contain information about endogenous but not synthetic ligands. The receptor infobox as you describe it sounds more like infobox about the ligands of a receptor rather than the receptor itself. As this lists of ligands can get quite long, I am skeptical if this information is appropriate for an infobox. I have no objection to creating a receptor infobox, but if one is created, IMHO, it should not duplicate information that is already contained in the gene infobox. Where I think a receptor infobox could be especially useful is for multi-subunit receptors. Boghog (talk) 19:51, 8 July 2018 (UTC)[reply]

I disagree. If you look back to the start of this discussion thread, it began as being about making pcol pages more accessible to the general reader rather than to the scientific specialist, and there were a couple of us who clearly expressed the view that general readers do not come here to learn about sequence homologies, but to learn about drugs and drug actions. Nobody is saying to list every ligand, but if we use the beta-2 receptor as an example since it was mentioned at the top, there should certainly be something about bronchodilators. What makes receptors interesting to the general public is their relevance to medicine, more so than whether they have multiple subunits. --Tryptofish (talk) 21:11, 8 July 2018 (UTC)[reply]

No where in the first paragraph does it mention ligands or pharmacological uses. Seppi moved the discussion here, but it just as well could have been moved to WT:MCB. The specific request was to add things like "where is that thing", "what does that thing do", "what makes that thing" to the gene infobox in beta-2 adrenergic receptor. That is to make the gene infobox more accessible to the general reader. The homologene link actually provides a partial answer to "where is that thing" (i.e., what species besides humans express the protein). The discussion was essentially hijacked by insisting it was solely about pharmacology. My top priority at the moment is making the gene infobox more readable relying on information already stored in wikidata. If others want create a new template, that's fine with me. My only request is that a new receptor template supplements but not replaces the gene infobox template. Boghog (talk) 21:47, 8 July 2018 (UTC)[reply]

Ah, ok I misunderstood what you meant Boghog. That doesn't seem like it would require too much time to code. I think what I've stated in my reply below should adequately address the issues mentioned above, although there is still 1 point of contention between the "Molecular mechanism" GO terms and creating a GPCR infobox for pharmacology information.

W.r.t. the scope of this discussion, the original idea I had was to cover both the pharmacology and molecular biology of a GPCR in 1 infobox. That's not ideal given what Boghog has stated about redundancy, so the GO terms should be used to cover the molecular biology in {{Infobox gene}} (caveat: see next paragraph); that's fine for that part. I also think that ranking the most importance GO terms as you've proposed would be very helpful. I agree with Tryptofish and still think that a separate infobox should be created for pharmacology data and cover information similar to IUPHAR's summaries for receptors in a GPCR family (e.g., scroll down to "Receptor", click "Show summary" for any one of these; that summary page can be somewhat messy at times since it includes experimental and radiolabeled ligands as well as binding data). They cover clinical uses of agonists and antagonists in the comments section. Taking into account what Tryptofish mentioned, a GPCR infobox should include fields for "Signal transduction", "Primary endogenous agonists", "Agonists", "Antagonists", "Inverse agonists", "Antagonist clinical use", and "Agonist clinical use"; the majority of that data should come from IUPHAR. For relevance to the general reader, the infobox should only include pharmaceuticals and other notable ligands and shouldn't list binding data like IUPHAR does.

W.r.t. the infobox for pharmacology data on GPCRs, I realize that "Signal transduction" and in some cases "Primary endogenous agonist" are covered by GO terms in the "Molecular mechanism" field of {{Infobox gene}}; however, there's two issues with using this to replace these two fields in the pharmacology infobox. The first is that the GO terms for GPCRs do not contain this data for any receptor within some GPCR families that have been characterized (e.g., compare "Principal transduction" and "endogenous agonists" in IUPHAR's entry with the any/all of the GO terms relevant to signal transduction and "[molecule] binding" in HCA1, HCA2, and HCA3; the GO terms are missing but the IUPHAR data on these is not). The second is that IUPHAR is – by a VERY wide margin – far more of an authority in this particular niche than the "experts" that assign GO terms. Case in point: they publish extremely detailed review articles on GPCR families, like this one for the HCA receptors. So, relying on GO terms for that data instead of IUPHAR seems like an incredibly bad idea. Seppi333 (Insert 2¢) 00:56, 9 July 2018 (UTC)[reply]

Please keep in mind, that the gene infobox covers all proteins, not just receptors. The world is broader than pharmacology. A big advantage of the GO terms is that is cover all proteins and provide consistency. Another advantage is that they provide a high level overview of the function of a protein that is appropriate for an infobox aimed at the general reader. Finally this data has already been loaded into wikidata and is accessible by mechanisms already in place. As I mentioned elsewhere, I am working to restore the link to the IUPHAR target database, so at the IUPHAR data will be only one click away. Longer term, we can work to capture and present data from IUPHAR, but this will be a lot more work (ligand → receptor data is already in wikidata, receptor → ligand data is not). Who is going to do this work? I also worry about how this will look. Receptors are complicated and there is a danger that we will overwhelm the infobox. Also please keep in mind that the original request was to make the data more understandable, not more complicated. Boghog (talk) 06:48, 9 July 2018 (UTC)[reply]

• They say that biology eats software (ref, ref); infoboxes eat everything in WP. What started as a discussion about readability has completely turned to infoboxness.

fwiw I have always viewed the MCB infoboxes as "data by biology geeks, for biology geeks". There is nothing there for the general reader, and I am actually fine with that.

With regard to mentions above about including agonists and antagonists, I would be somewhat rabidly opposed to pulling that from Wikidata - anything about drugs or diseases. We had a brouhaha about those fields in Wikidata after some yahoo over there ran a bot that added a big import of data from ChEMBL into Wikidata where they populated the "drugs used to treat" field with chemicals that were hits in HTS or that had activity based on in vitro or animal experiments - all kinds of chemicals (discussed here); I also noted here that weird data was added to Wikidata such that we got "diseases associated" with "ligands" via entries in gene/protein items in Wikidata. Not good.

So please do not use Wikidata to auto-generate infoboxes where we end up presenting the public with health claims. The infobox-gene is fine now, as is it. Jytdog (talk) 02:20, 9 July 2018 (UTC)[reply]

The initial complaint was about the readability of the gene infobox. It didn't turn into a discussion about infoboxes, that's where it started. I agree with you that the information in the gene infobox is primarily for MCB geeks and there is nothing wrong with that. But with some work, we could also make the information more accessible to the general reader so that it serves both audiences. I already mentioned above the concerns about medical claims by pointing to this discussion. Simply listing agonists and antagonists is not a medical claim. Listing their therapeutic uses is a medical claim. Boghog (talk) 05:46, 9 July 2018 (UTC)[reply]

I feel like we are talking past each other, and I have this suggestion: the gene infobox is probably fine for its intended purpose, but the request for a receptor infobox that is not (quoting the OP) "very difficult to read and lacking key information" could be addressed by creating a new infobox for receptors that would be like what Seppi described just above. So, a gene infobox for the geeks, and a receptor infobox for the general lay reader. --Tryptofish (talk) 20:08, 9 July 2018 (UTC)[reply]

Boghog: The OP said Wondering if I could pick your brain. I often use WP as revision and for my work as I'm sure many people do. I find many of our articles (e.g. Beta-2 adrenergic receptor, which I'm looking at now) very difficult to read and lacking key information which (I feel at least) could be included in the infobox - e.g. where is that thing, what does that thing do, what makes that thing). I don't want to reinvent the wheel discussion wise so I thought I'd ask if any of those discussions have happened before, and what do you think about some sort of approach to making these articles somewhat more readable?. That is about badly written WP:LEADs. Per WP:MCBMOS all that information should be in the body and should be nicely summarized in the lead, right? Looking to solve basic editing problems by some kind of Wikidata-driven infobox workaround, is as problematic and bad of an idea, as the WMF making the unilateral decision to create "short descriptions" for mobile and apps, using the field from wikidata, because our first sentences are so badly written and cluttered. Jytdog (talk) 20:33, 9 July 2018 (UTC)[reply]

Sorry, I stand corrected. The original request was to make the article more understandable by including key facts in the infobox. I agree with you that an infobox is no substitute for a well written lead. At the same time, a well designed infobox can provide a useful, at a glance summary of the subject. In cases where the lead is deficient, an infobox can highlight those deficiencies and inspire editors to fill in the gaps. Boghog (talk) 21:19, 9 July 2018 (UTC)[reply]

Tryptofish, I am fine with other infoboxes being created, as long as they do not use Wikidata to generate health claims (so no association with diseases or drugs used to treat or dietary substances that affect, or whatever) Jytdog (talk) 20:33, 9 July 2018 (UTC)[reply]

I agree. --Tryptofish (talk) 22:33, 9 July 2018 (UTC)[reply]

Actually that quote refers to the article, not the infobox. The proposed revision to the gene infobox would contain the key fact table above and collapse the gene location and RNA expression sections. We haven't seen any mock ups of a receptor infobox yet, so it is premature to say which will be more understandable to the general lay reader. It would be equally valid to assume that a receptor infobox would be for pharmacology geeks. Boghog (talk) 21:09, 9 July 2018 (UTC)[reply]

? Right. That is what I said in my post - the OP was about the readability of articles. You wrote above in response to me, The initial complaint was about the readability of the gene infobox but that was not accurate. Hence my response to you. Dealing with problems of readability of articles by an infobox trick, is ducking the problem. Jytdog (talk) 21:13, 9 July 2018 (UTC)[reply]

Did you read my response to you above? Boghog (talk) 02:52, 10 July 2018 (UTC)[reply]

I did, thanks. It remains remarkable to me that almost none of the discussion has focused on the actual problem of article readability but instead zoomed right into the proposed solution of infoboxes. Infoboxes eat everything. :) Jytdog (talk) 19:41, 13 July 2018 (UTC)[reply]

So... are there any objections to the creation of {{Infobox GPCR}} with manually-populated/user-supplied fields for |signal transduction=, |primary endogenous agonist(s)=, |agonists=, |antagonists=, |inverse agonists=, |antagonist clinical use=, and |agonist clinical use=? If not, I'll probably create it sometime within the next few days. Again, this infobox is mainly intended for these articles: Rhodopsin-like receptors. Seppi333 (Insert 2¢) 08:30, 13 July 2018 (UTC)[reply]

@Seppi thanks for proposing this. I feel it would be better to have a more generic {{Infobox receptor}} with subfields also including:

• "type" (e.g. G protein coupled)
• "cellular location" (e.g. membrane, cytoplasmic, nuclear") field
• "cellular action" (e.g. how the receptor works within the cell)
• "organs" (which organs its expressed in, not too fussed on name)
• "effect" (what the overall effect of action is, not too fussed on name)--Tom (LT) (talk) 09:46, 13 July 2018 (UTC)[reply]

Based upon the enormous discussion/wall of text above, Boghog pointed out that fields like "cellular location/action", effect, and organs (expression pattern) are already included in {{Infobox gene}} under "Gene ontology" and "RNA expression pattern", so it'd be redundant to include those in a 2nd infobox. The only reason I'd like to limit this to GPCRs is that all of these proposed fields need to be populated manually; given that there are thousands of receptor proteins and only a couple hundred non-olfactory rhodopsin-like GPCRs, limiting the infobox to those articles requires much less work to implement relative to all articles on nuclear receptors, LGICs, GPCRs, RTKs, and the like.

I can't possibly be the only one. See estrogen receptor or Beta-2 adrenergic receptor. There are definitely no fields which say that those things do or where they are. There's just a lot of links and numbers. No words. This is a problem which needs solving. All the people who aren't biochemists - which includes students of primary, middle, high school, undergraduates, lay people, medical professionals, other biomedical professionals, patients, and other people who have for some reason stumbled upon these articles finds these infoboxes completely useless. This is not the encyclopedia we should aim to be. --Tom (LT) (talk) 11:09, 13 July 2018 (UTC)[reply]

We can roll out a receptor infobox using some sort of automated tool to make this easier, e.g. AWB. The problem that I think we should try and solve is that there's some crucial information that's missing from receptors, and that this is not readable for untrained humans. --Tom (LT) (talk) 11:09, 13 July 2018 (UTC)[reply]

Revised reply (fairly passionate about this topic as you can see). Yes I agree with your proposal. Better to start somewhere. Depending how this goes we can expand the template as needed. --Tom (LT) (talk) 14:02, 13 July 2018 (UTC)[reply]

That said, I'm assuming the "effect" field you're thinking of is more relevant to the clinical effects of receptor agonists, correct? If so, something like |Agonist clinical effect= might be useful to include. Using beta-2 adrenergic receptor as an example, this infobox could be populated with input like |Agonists=Salbutamol, etc., |Agonist clinical use=Asthma, etc., |Agonist clinical effect=bronchodilatation, etc. (NB: the term "clinical effect" here refers to a "therapeutic effect" for a particular use, not its side effects). Seppi333 (Insert 2¢) 10:14, 13 July 2018 (UTC)[reply]

@Seppi333 Definitely not. I'm talking about its physiological action. That should definitely be included as it is, after all, the evolutionary purpose for something in the body. The reader can then interpret the clinical effect themselves or via text --Tom (LT) (talk) 11:09, 13 July 2018 (UTC)[reply]

I agree with Tom (LT) that the scope of the receptor infobox should be wider than GPCRs. I also agree with Tom (LT) that the emphasis should be placed on more general concepts like physiological function (what it does), signal transduction pathways (how it does it), and tissue and subcellular distribution (where it is). Concerning ligands, I think there is a clear hierarchy of importance. By far, the most important are endogenous ligands. Second would be clinically validated/approved drugs that can pass WP:MEDRS muster. The third would be widely used research tools supported by secondary sources. Finally in analogy to {{Infobox neurotransmitter}} which was eventually subsumed into {{infobox drug}}, I suggest that the proposed {{infobox receptor}} eventually be subsumed into {{infobox gene}}/protein. Boghog (talk) 17:26, 13 July 2018 (UTC)[reply]

I suggest that the proposed {{infobox receptor}} eventually be subsumed into {{infobox gene}}/protein. - that is an outstandingly good idea. Also, I agree that this infobox should be wider than GPCRs since confining it to rhodopsin-like receptors misses notable neurotransmitter receptors like the metabotropic glutamate receptors and nicotinic acetylcholine receptors; I just don't really see how we could use an infobox with the same fields as above to populate a receptor infobox for a number of receptors like alpha-4 beta-2 nicotinic receptor given that we'd need to account for variation in a ligand's affinity relative to the receptor's stoichiometry (a 2nd trivial consideration is that the infobox would need to also include a field for "Channel blockers" of the LGIC's ion channel). Anyway, it just occurred to me while writing this that |Positive allosteric modulators=/|Negative allosteric modulators= would be appropriate to include as parameters for relevant GPCRs in {{Infobox GPCR}}. Seppi333 (Insert 2¢) 17:42, 13 July 2018 (UTC)[reply]

With apologies for my limited understanding of how infoboxes work, I have a concern about "subsumed". If, as I suspect, it simply means that all of the parameters for each infobox will become available within a single infobox (so that editors could choose which fields to fill in for a given page), that's fine with me. But I just want to make sure that it doesn't mean that the receptor parameters would be lost. --Tryptofish (talk) 18:44, 13 July 2018 (UTC)[reply]

Yes, that is what I meant. All the parameters from the daughter infoboxes would also be available from the parent with the possible exception of overlapping parameters that might be merged and/or renamed. Boghog (talk) 21:20, 13 July 2018 (UTC)[reply]

Thanks, sounds good. --Tryptofish (talk) 22:20, 13 July 2018 (UTC)[reply]

Am opposed to the |Agonists=, |Antagonists=, |Inverse agonists=, |Antagonist clinical use=, and |Agonist clinical use= fields, especially the latter two. They will be filled with garbage from ChemBL and the like in Wikidata, that will then come into WP. The proposed "effect" as well as "Agonist clinical use" and "agonist clinical effect" fields are also dangerous. We saw this movie before. They would be OK if they are filled manually-only, not sourced from Wikidata. Jytdog (talk) 19:42, 13 July 2018 (UTC)[reply]

Wikidata does have the ability to rank data (Deprecated/Normal/Preferred) and infoboxes can be configured to only display Normal/Preferred or only Preferred data. With a minor amount of work, {{infobox gene}} could also be configured this way so that at a minimum, if there was questionable data, it could be manually Deprecated and therefore not displayed. What I was proposing with the GO data is to manually assign Preferred data and only display Preferred data. What is being proposed (I think) with {{infobox receptor}} is to manually select data from IUPHAR target database. If {{infobox receptor}} were later subsumed into {{infobox gene}}, the manually curated data from the {{infobox receptor}} would be transfered into wikidata and then displayed in {{infobox gene}}. I do realize that this manual curation is a lot of work, but if it were done one receptor family at a time, because of similarities between family members, the process could be speeded up considerably. Boghog (talk) 21:47, 13 July 2018 (UTC)[reply]

I hear all that and that is all fine to me, as far as it goes. For the first step of that (IUPHAR >> infobox receptor), the hardest thing consensus-wise from mu view would be agreeing on what fields need MEDRS refs. Say that gets done and the data gets imported, for step 2 (infobox receptor >> >>wikidata >> infobox gene) the question of how to prevent somebody else from running bots in Wikidata that screw it up will come into play. There was an interesting notion raised in the Wikidata RfC about drawing infoboxes from a "locked" clone of Wikidata, rather than from the wild-west live version.... Jytdog (talk) 23:07, 13 July 2018 (UTC)[reply]

Agree that the implementation here is key. In general I think it's important to include as above endogenous ligands at the very least. We have to be careful about clinical agonists/antagonists. It should for starters only include clinical classes, which is useful to know, and not specific drugs, which will produce a long list and is not. It should have some clearly defined criteria about whether we are going to include a very lengthy list of drugs that have some partial or crossover activation or not. --Tom (LT) (talk) 23:38, 13 July 2018 (UTC)[reply]

Parameters are:

• |name= (infobox name defaults to {{PAGENAME}} if excluded)
• |signal transduction=
• |primary endogenous agonist= OR |primary endogenous agonists= (produces single vs plural output)
• |agonists=
• |agonist clinical use=
• |antagonists=
• |antagonist clinical use=
• |inverse agonists=
• |PAMs=
• |NAMs=
• |IUPHAR Target ID=

It needs some formatting tweaks to match the width of {{Infobox gene}} (that's slightly wider) and make it look pretty, but you get the idea of how it will look/work. Also, I had no idea GPCRs could couple to both G_s and G_i/o. Seems rather counteractive. Seppi333 (Insert 2¢) 10:07, 15 July 2018 (UTC)[reply]

In general, I like it! About your question about G protein coupling, my impression is that it would be like Gs in one kind of cell and Gi in another kind, or maybe that some other modulator would switch it from one to the other (although I could be incorrect), but that it wouldn't be both simultaneously in the same cell. --Tryptofish (talk) 17:39, 15 July 2018 (UTC)[reply]

I think you will need to get some kind of buy-in that IUPHAR complies with MEDRS with respect to at least the "agonist clinical use" and "antagonist clinical use" fields.

To that point, I don't understand why the "antagonist clinical use" field is N/A, and the "agonist clinical use" field is incorrect with regard to the first agonist that is listed. Jytdog (talk) 17:57, 15 July 2018 (UTC)[reply]

Those fields pertain to selective agonists/antagonists; the first agonist is not selective. IUPHAR covers FDA-indicated uses, so the MEDRS issue isn’t really relevant if one uses IUPHAR to fill these parameters. The input for clinical uses comes from [1], specifically: Short (salbutamol, terbutaline) and long (formoterol, salmeterol) acting β2-adrenoceptor-selective agonists are powerful bronchodilators used to treat respiratory disorders. Many first generation β-adrenoceptor antagonists (propranolol) block both β1- and β2-adrenoceptors and there are no β2-adrenoceptor-selective antagonists used therapeutically. Seppi333 (Insert 2¢) 19:20, 15 July 2018 (UTC)[reply]

Perhaps it would be better to just prepend “selective” to those fields. Seppi333 (Insert 2¢) 19:48, 15 July 2018 (UTC)[reply]

I don't know where all the places are, that IUPHAR gets content about "clinical use". Before rolling this out please get consensus that IUPHAR is reliable per MEDRS for that content. Jytdog (talk) 20:03, 15 July 2018 (UTC)[reply]

I find pharmacology and biochem super interesting, cool to see a community of people who do too. — Preceding unsigned comment added by Chemotron (talk • contribs) 07:06, 4 July 2018 (UTC)[reply]

Welcome to Wikipedia, and to WikiProject Pharmacology! Let me know if you ever need any assistance with anything! There's tons of work to do, so feel free to be WP:BOLD and dive in! ―Biochemistry🙴❤ 17:23, 4 July 2018 (UTC)[reply]

Thank you! Is there anything I can help with? --Chemotron (talk) 22:08, 4 July 2018 (UTC)[reply]

See Wikipedia:WikiProject Pharmacology#How to help; there's plenty to do on the cleanup list! Klbrain (talk) 22:36, 4 July 2018 (UTC)[reply]

Please see discussion at Wikipedia_talk:WikiProject_Medicine#Level_of_reading_dispute; input very welcome. Jytdog (talk) 13:26, 9 July 2018 (UTC)[reply]

The scope of the problems with this article's comprehensiveness pertains more to WP:MCB; however, synthetic antioxidants are within this project's scope, so I'm liking this here: Wikipedia:Featured article review/Antioxidant/archive1. There's currently a total of 7 sentences relevant to drugs in this article under Antioxidant#Drug candidates. Seppi333 (Insert 2¢) 02:19, 11 July 2018 (UTC)[reply]

I'm requesting feedback on article content in nootropic. The issue is described at Talk:Nootropic#Coverage of CNS stimulants. Another editor and I are engaged in an edit war, so we need unbiased third-party feedback on the disputed content. Seppi333 (Insert 2¢) 07:52, 13 July 2018 (UTC)[reply]