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Happy New Year, Boghog!

Happy New Year!

Boghog,
Have a prosperous, productive and enjoyable New Year, and thanks for your contributions to Wikipedia.
— Moops ⋠T⋡ 03:11, 2 January 2023 (UTC)

   Send New Year cheer by adding {{subst:Happy New Year fireworks}} to user talk pages.

— Moops ⋠T⋡ 03:11, 2 January 2023 (UTC)

Hej Moops. Thanks a great new year to you! Boghog (talk) 18:47, 2 January 2023 (UTC)

I have reverted your edit...

Saygin D, Tabib T, Bittar HE, Valenzi E, Sembrat J, Chan SY, et al. (2013). "Transcriptional profiling of lung cell populations in idiopathic pulmonary arterial hypertension". Pulmonary Circulation. 10 (1): 132–136.

Hi @Boghog, a couple of hours ago you have input a text (provided above) in the Tyramine article for six (!) times, rewriting references... I view that as spam. So, I had to revert your edit. Tosha Langue (talk) 08:35, 16 January 2023 (UTC)

@Tosha Langue: Thanks for your message. My edit was not intentional spam, but rather a bug is a script that I was using. The problem is that PubMed has recently started returning close matches for DOI searches. I previously fixed the bug, but I forgot to update the script on another workstation that I am using. Sorry about that. Boghog (talk) 08:54, 16 January 2023 (UTC)

TFA nom for enzyme inhibitor

I have nominated enzyme inhibitor to be today's featured article for a non-specific date. You are invited to comment on this nomination by clicking here. Z1720 (talk) 04:02, 9 February 2023 (UTC)

BPI fold proteins/genes

tldr: how to get the "Infobox_gene" template/tag to work when it isn't automatically self-implementing, and a good way to deal with important functional genes in non-human species that are merely pseudogenes in humans?

Hi. Because I had been doing external work that related to this gene family, I started cleaning up, expanding, and authoring WP pages on the whole family. I saw you did clean-ups of my edits on a few of those pages and I'd like to thank you for that. You did another thing which was a good idea that I'm implementing throughout the pages of this group of BPI fold proteins/genes -- setting aside the section about what defines a BPI protein and how they are all related as a separate "Superfamily" section. I don't know why I didn't think of that myself, it's kind of obvious. Anyway, since you have an interest, I hope you can help me with two things about the "Infobox_gene" template/tag.

First, I know that background WP scripts scrape sources like NCBLI's entrez/gene/genbank/nucleotide/pubmed/etc, Ensembl, Genecards, Uniprot, etc to eventually generate that useful Infobox that organizes links to the technical data and resources. So, what happens when that background process fails? Is there a simple way to force the process? For example, when I've applied that template/tag before it took min to hrs to self-implement but that hasn't worked when I applied it to the BPIFB3 page. I briefly looked into how and what the scripts do but I'm not capable trying to rewrite WP code without breaking a lot things. The external source data exists for sure, others and I have cited them in that BPIFB3 WP page. What can you suggest or point to others with a solution to get the "Infobox_gene" box to work?

Second, there's ambiguity on how best to author a page on a protein/gene that is present on some species but not others, particularly with the human-centric bias of WP. At a certain level many of us scientists necessarily ignore a human-centric view of life, so it's actually important. In the case of BPIFB5, it's present in humans only as a pseudogene (BPIFB5P) but is a perfectly useful protein in other mammals like the mouse and apparently there's multiple publications on bovine BPIFB5 plus an anti-BPIFB5 (cow) antibody that's commercially available right now. But more relevant to WP's scraping of genomic databases is the mouse for which there's a wealth of support for accessing mouse genome data. So what your opinion on the the best way to deal with this issue? I opted to author a BPIFB5 page on the basis of the BPIFB5P human pseudogene, partly because (1.) the most information about this superfamily is in the human biomedical literature so I'm simply conforming to the foundational references that describe the BPIF family and tend to highlight BPIFB5 in its form as a human pseudogene, (2.) I made a "standardized" figure based on that and am re-purposing versions of it for the other WP pages in this family and don't want to mess with it, and (3.) I had assumed the "Infobox_gene" template/tag works in concert with the "Short description" template/tags and included the "Short description|Pseudogene in the species Homo sapiens" to facilitate the self-implementation of the "Infobox_gene" box -- but I now realize the assumption was wrong. Alternatively, I believed I could have authored a BPIFB5 page as a mouse protein page, tagging it with "Short description|Protein-coding gene in the species Mus musculus" and then mentioning the human pseudogene in the article's text... and in doing so, I would hope the "Infobox_gene" template/tag would find the mouse genomic data to populate an Infobox. Would that work? I don't know, maybe it would suffer a similar failure to the BPIFB3 page, as above.

This last point is not an empty, academic exercise because the issue is going to come up again and it would be good to have an efficient solution. There is another family member, BPIFB9 which has functional proteins/genes in other mammals but is a BPIFB9P pseudogene in humans. There's multiple publications on rodent BPIFB9 (a.k.a. vomeromodulin). Unlike BPIFB5 above, which is a relatively minor protein, vomeromodulin is a major player in chemical olfaction as a pheromone transporter in non-human mammals, reflected by the commercial market for BPIFB9 peptide and antibody products. So authoring an article on this as a human pseudogene doesn't make that much sense, but failing to get the "Infobox_gene" to work for mouse/rat genome information wouldn't be good either. And this whole note has been about BPIF-B but there's the fragmentary WP pages BPIF-A coming up next which also have the non-human gene vs human pseudogene issue. Lapabc (talk) 18:26, 13 February 2023 (UTC)

Hi. Thanks for your message and for your contributions! The short answer to your question is Wikidata. Data for most human genes has already been scraped from Entrez and other sources and uploaded into Wikidata. {{infobox gene}} has been configured to download this data, but only after the corresponding Wikipedia page has been registered in Wikidata. For BPIFB5P, I did this in this edit. On the Q20785867 page, scrowl down to Wikipedia, edit, and add the language (Englsh) and enter BPIFB5P. After this is done, {{infobox gene}} will download the relevant Wikidata data and display that information in {{infobox gene}} in Wikipedia. Cheers. Boghog (talk) 19:01, 13 February 2023 (UTC)
Thanks! I knew about Wikidata but not how to deal with it. When I get a chance later I'll use your method to fix BPIFB3. Lapabc (talk) 19:19, 13 February 2023 (UTC)
Concerning genes/proteins that are present in some species but not others, the main issue is the gene present in humans or not. If in humans, use {{infobox gene}}, if not, use {{infobox nonhuman protein}}. If in human, the lead sentence the "protein X" is a protein that in humans is encoded by the "Y gene". This wording implies that the gene may also be expressed in other species. There is a HomoloGene link in {{infobox gene}} that will define what other species this gene exist. Boghog (talk) 19:17, 13 February 2023 (UTC)
Good to know about {{infobox nonhuman protein}}, thanks again. So your opinion, please... (1) author a single BPIFB-9P human pseudogene page that also discusses rodent BPIFB-9a briefly, (2) author a single BPIFB-9a/vomeromodulin page that mentions the human BPIFB-9P pseudogene, or (3) author two pages, one for each gene. Number 3 seems the best but I'm leaning to number 1 because, honestly, it's a lot less trouble for me. Lapabc (talk) 19:39, 13 February 2023 (UTC)
Generally we try to devote one page to one gene. This page would also include orthologs in other species as defined in HomoloGene. However with larger, more notable gene families, we have in additon have gene family pages. In this case, option #1 seems to make sense. Cheers. Boghog (talk) 11:17, 17 February 2023 (UTC)
Hi again. Just a quick question about the {cite journal} "|vauthors=a,b,c|" format vs the "|last1=x|first1=y|" format. I see you keep changing things to the vauthors format. I'm using the automatic template from the editor's pull-down menu which automatically produces the |last|first| format. Manually changing that too big a hassle so will there ever be an option option for people to automatically do the vauthors format? Is this a new style preference that I should be concerned about?Lapabc (talk) 08:58, 17 February 2023 (UTC)
Hi. Actually |vauthors= is an old style preference. User:ProteinBoxBot that populated original 5000+ set of Gene Wiki articles followed the Vancouver system authors. I am just trying to keep the citation style of new articles that transcribe {{Infobox gene}} consistent with the older articles. One tool that can be used to create citations that follow this format is Wikipedia template filling. Just paste in PMID or PMC id, and the tool will create a fully populated citation template that can be copied and pasted into the article. Cheers. Boghog (talk) 11:12, 17 February 2023 (UTC)
I took a look, bookmarked it, and will use it for the remaining WP pages on BPIF family I plan to finish. Cheers back to you. 18:30, 17 February 2023 (UTC) Lapabc (talk) 18:30, 17 February 2023 (UTC)

Seems like the article is again being vandalized by a Sockpuppet to avoid the block

I am not very familiar with Wikipedia's reporting processes, and the article in question "African admixture in Europe" is not among the articles I usually edit.

If you could help to fix the current block evasion and sockpuppeting of the new IP of the blocked User:Guran223 in the article I'd be grateful.

Thanks. Venezia Friulano (talk) 15:10, 18 February 2023 (UTC)

Hi @Venezia Friulano: I don't have much experience with handling sock puppets, but I haved created an entry here. I am not sure that I got the details correct, so please feel free to edit the entry. Cheers. Boghog (talk) 15:46, 18 February 2023 (UTC)

Citation damage

@W van Wyk: and I have reverted citation damage to Glyphosate-based herbicides. Most notably falsifying 2 unrelated citations to the unrelated "Programming pluripotent precursor cells derived from Xenopus embryos to generate specific tissues and organs". Your bot changed doi:10.3390/f8060208 and in a different location doi:10.3390/jmse8060399 to this unrelated publication. The dois are correct and do not correspond to any of the bibliographic information your bot substituted. I must say this is a new low. Invasive Spices (talk) 21:04, 9 February 2023 (UTC)

The "falsifying" of the two references is a result that PubMed has recently started returning close matches for DOI searches and to my knowledge, they have not documented this change and more importantly how to test for it. I recently added a test for this condition, which caught most but not all these errors. I now have added an additional test that should catch the remainder of these errors. Boghog (talk) 06:31, 10 February 2023 (UTC)
You need to begin accepting responsibility for your own edits. If the admins were not actively and passively encouraging you they would have told you that long ago. Invasive Spices (talk) 21:43, 21 February 2023 (UTC)
I absolutely do accept responsibity of my own edits. I as everyone else make occasionally makes mistakes and I correct them as I find them. Boghog (talk) 03:57, 22 February 2023 (UTC)

Title

You deleted Pelot, Daniel, (M.D.)'s title from Ranitidine. Error? Tanishism (talk) 22:44, 24 February 2023 (UTC)

Hi. Actually, the deletion was intentional. Per MOS:CREDENTIAL and MEDMOS Do not hype a study by listing the names, credentials, institutions, or other "qualifications" of their authors. Also the article follows the Vancouver system of author format which is last name followed by first and middle initials. Vancouver style authors do not include medical or academic degrees. Inserting degrees (Pelot D M.D.) into the |vauthors= parameter of {{cite book}} will generate an error message (Vancouver style error: punctuation in name). The vauthors will accept "Pelot D MD" but will polute the metadata since "Pelot D" will be treated as the last name and "MD" will be treated as first and middle initials. Boghog (talk) 07:26, 25 February 2023 (UTC)

Citation change

It appears that this edit mixed up citations.

The original citation was a blend of two citations in one. The pmid was for one citation and the doi and s2cid were for another. The pmid field contained the pmc value. It looks like the changes were made based on the pmid. The pages and date in the orignal appear to be wrong too. Also, the replaced citation is missing the language field (French).

The citation bot ran before your edit and it didn't fix it.

The original was

P N Leigh; D Jefferson; A Twomey; C D Marsden (August 1985). "Beta-adrenoreceptor mechanisms in essential tremor; a double-blind placebo controlled trial of metoprolol, sotalol and atenolol". J Neurol Neurosurg Psychiatry. 46 (8): 510–15. doi:10.1136/jnnp.46.8.710. PMID 1027523. S2CID 12506398.

and it was replaced by

Aliperta A, Saviano G, Bellissimo U, Perna A (August 1985). "[Importance of etiopathogenic factors on the characterization of phlogistic changes in the bronchi]". Broncho-Pneumologie. 26 (6): 498–503. doi:10.1136/jnnp.46.8.710. PMID 1027523. S2CID 12506398.

It looks like the original text replacing the pmid with 6310053 and its associated date and pages is the intended citation.

Leigh PN, Jefferson D, Twomey A, Marsden CD (August 1983). "Beta-adrenoreceptor mechanisms in essential tremor; a double-blind placebo controlled trial of metoprolol, sotalol and atenolol". Journal of Neurology, Neurosurgery, and Psychiatry. 46 (8): 710–15. doi:10.1136/jnnp.46.8.710. PMC 1027523. PMID 6310053. S2CID 12506398.

--Whywhenwhohow (talk) 00:50, 27 February 2023 (UTC)

Can your tool verify that the pmid and doi are congruent before making any changes? The replacement had the wrong doi and s2cid. --Whywhenwhohow (talk) 01:00, 27 February 2023 (UTC)
Thanks for pointing out the error and for the suggestion. My script assumes that the pmid is correct and in the above case, it wasn't. As you suggest, I will modify the script to make sure that the returned citation also matches the doi if present. For good measure, the script should also compare some of the other fields. More later. Boghog (talk) 06:13, 27 February 2023 (UTC)

wow!

How did you fix these dead link citations ? I d like to know . Thanks. Wuerzele (talk) 20:08, 1 March 2023 (UTC)

Hi, thanks! I fixed the dead links by typing the link into the Wayback Machine. That website then returns a list of dates for which it has archived the link, for example. Pick a date with a blue circle. You may have to go back to previous years. It will then return a archived URL. Cheers. Boghog (talk) 20:29, 1 March 2023 (UTC)

Disruptive citation bot

Your bot is removing some parameters from citations. In this edit specifically, it has removed the url parameter from the JAMA reference. It has changed the date of the JAMA reference from "December 15, 1989" to "December 1989". It has also removed the wikilinks to JAMA and Indian Journal of Ophthalmology. It has also removed the issn parameters from four other references. I don't know if this one was intentional, but it has change a journal parameter to "journal = The Canadian Journal of Infectious Diseases = Journal Canadien des Maladies Infectieuses". Removing important parameters like the url and date is extremely disruptive. Please deactivate your bot until this issue is resolved. It seems to be doing more harm than good. Mudsk (talk) 20:01, 8 March 2023 (UTC)

Hi. The |url= parameter is redundant to the |doi= parameter. Both doi:10.1001/jama.1989.03430230122038 and https://jamanetwork.com/journals/jama/article-abstract/379907 point to the same web page. The advantage of a DOI is persistence; the DOI should continue to direct a reader to its assigned resource in perpetuity, whereas a URL may change. The official full name of the Candadian journal is both English and French. I don't see the problem in adding the French translation to the English. The script did not remove the date parameter. It just truncated "December 15, 1989" to "December 1989". Why link journal names? This contributes to a MOS:SEAOFBLUE where a large portion of the citation is externally linked and starts to look like WP:Blue Sea with a sea of blue. The script also made additional edits like adding missing authors, location, and publishers, replacing cryptic |website= with more readable |publisher=, and standardized the display of authors. Boghog (talk) 21:01, 8 March 2023 (UTC)
Okay, I'm sorry I hastily criticized your script. I shouldn't have jumped to conclusions. It would be useful if you could document what it does and the reasons somewhere in your userspace and link to it in the edit summary for me and others who may come across your script.
Although I still have some questions. Why does it remove the issn parameter? Even if issn and doi link to the same page, don't they contribute to the metadata of the citation? Is linking their only purpose? When the article is viewed offline, either printed or with Kiwix, won't it make sense to have the complete metadata such as issn, doi and url in that case?
What is the point of truncating the date?
I've also just noticed that it has removed access=subscription from the JAMA reference, what's the reason for that?.
In Template:Cite journal#Periodical, they've specifically mentioned that the work parameter may be wikilinked. Linking the journal name to it's article allows the reader to know which references are more notable than others. Even templates such as Template:CDC and Template:Gray's link to the the respective Wikipedia articles. Mudsk (talk) 05:43, 9 March 2023 (UTC)
According to the {{cite journal}} documentation, Specify the DOI to provide a permanent link, and an URL where the article is free. In the case of the JAMA reference, the URL is not free. It is also redundant to the DOI. More is not necessarily better. It can be distracting. But I have re-added it. 25 years after the reference was published, is someone really going to worry about which exact day of the month the article was published? The point of truncating the data is consistency with the rest of the citations in the article. Quite often, only the year of publication is included in citations. Including also the month seems like a good compromise. Before my edit, only a few of the |issn= for {{cite journal}} citations were included. I have now added issn values for all the journal citations. Currently there is no |journal-link= parameter in {{cite journal}}. I will work on some documentation and include a link to it in future edits. Boghog (talk) 09:46, 9 March 2023 (UTC)

non peer reviewed references

Why does a source have to be peer reviewed to post information on wikipedia? Is there a rule? Furthermore, the NIH accepts preprints as publications for reviewing grants, is wikipedia held to a higher standard than the NIH? The point is that the information is published and anyone can look at it and dispute its veracity. If one identifies a problem with the source and it is a preprint, of course remove the information. But if a contributor cannot make any reasonable claim to an inaccuracy, then it is a valid source, no? Wikipedia should be the most up to date source of information. It can take years to publish an article. I believe waiting for peer review harms wikipedia and is contrary to its purpose to be a real time encyclopedia. PhD2005 (talk) 20:38, 17 March 2023 (UTC)

Hi. According to WP:SCIRS, a peer reviewed source is normally the miminimum required to support a scientific claim. Even this is not ideal. A secondary source (review article) is preferable. This applies not only to scientific aricles, but is a Wikipedia policy for all articles (see WP:SECONDARY). Futhermore, according to WP:MEDRS, secondary sources are needed to support medical claims. Why is this? Two reasons. The first is the replication crisis. An astonishing high percentage of biomedical research simply cannot be repeated. It is therefore important that the finding be reviewed and put in context of related research. This double review process doesn't catch all errors, but reduces them. The second reason is WP:NOTABILITY. If a finding has been reviewed by an independent reviewer, then the finding is more likely to be notable. The difference between the NIH and Wikipedia is timing. When the NIH is evaluating a grant application, it needs access to the most recent work from that group to put the application in context. Furthermore, the NIH review pannel is a form of peer review. Wikipedia in contrast prefers not to cover lastest breaking results, but rather wait until the finding has been covered in a review article. Boghog (talk) 21:15, 17 March 2023 (UTC)
The mission of the NIH is to push the boundaries biomedical research. The purpose of Wikipedia is to report facts. Boghog (talk) 06:10, 18 March 2023 (UTC)

Senate Pact 2023

Hi Boghog. Could you have a look at the article Senate Pact 2023? I mean the infobox’s Pact members section; I wanted to make "Civic Coalition", "The Left" and "Polish Coalition" collapsible to allow hiding/showing their contents (see Template:Collapsible list) instead of a horizontal list (with brackets) but keep "The Left" and "Polish Coalition" non-bold text. I.e., "Civic Coalition", "New Left" and "Polish People’s Party" should be bold. I hope you don’t mind I messaged you; I am probably too dumb to do that correctly, haha. Thanks in advance! Regards, TaurenMoonlighting (talk) 10:55, 21 March 2023 (UTC)

Hi TaurenMoonlighting. Is this what you had in mine? Cheers. Boghog (talk) 14:44, 21 March 2023 (UTC)
Thanks for the reply! Partially, yes but I wanted to bold: "Civic Coalition" (as a whole), "New Left" (within The Left), "Polish People’s Party" (within Polish Coalition), and "Poland 2050"; while keep as non-bold, regular text: "The Left", and "Polish Coalition". That’s because according to the agreement Civic Coalition, New Left, Polish People’s Party, and Poland 2050 have the right to propose candidates for Senators. However, even if I delete the apostrophes, Template:Collapsible list automatically bolds "The Left" and "Polish Coalition" as headings. Is there a way to unbold them, i.e. to force displaying them as regular text via some additional parameters (while keeping the list collapsible)? It’s a bit hard to explain what I mean, but I hope you’ll understand :-) Also, there is a small error; "Poland 2050", and "Yes! For Poland" are completely separate entries (i.e., "Yes! For Poland" should be a fifth one, but non-bold). I wish I could show what I have in mind rather than describe it, but I tried my best, hahah. Thanks very much for the help, I appreciate it! TaurenMoonlighting (talk) 17:43, 21 March 2023 (UTC)
I am having difficulty following the hiearachy. Is the following accurate?
  • Civic Coalition
    • Civic Platform
    • Modern
    • Polish Initiative
    • The Greens
  • The Left
    • New Left
    • Left Together
    • Polish Socialist Party
    • Labour Union
  • Polish Coalition
    • Polish People's Party
    • Union of European Democrats
    • Centre for Poland
    • Silesians Together
    • Fair Play Country
  • Poland 2050
  • Yes! For Poland

If not, please edit. Also if "Yes! For Poland" is seperate from the other subheadings, then in my opinion, it should be bolded. Boghog (talk) 18:11, 21 March 2023 (UTC)

I’ve edited the list to make it look as I wanted. Still, I would like the sub-coalitions to be collapsible. The reason why these 4 entries should be bold is because they have the right to divide candidates for Senators (i.e., the Civic Coalition as a whole has its own "portion", and the New Left, not The Left as a whole, has its own to divide between the rest of The Left, etc.). As for the Yes! For Poland, they’ll also recommend candidates, but according to the agreement (its full text can be read at ref 2) they don’t have a "portion" of mandates. Additionally, Yes! For Poland’s representative Z. Frankiewicz serves as Senate Pact 2023’s organizer. TaurenMoonlighting (talk) 18:45, 21 March 2023 (UTC)
OK, thanks. I am still a little confused as why should sub categories (e.g., New Left) but not categories be bolded? Boghog (talk) 20:06, 21 March 2023 (UTC)
Yeah, I can imagine it might be confusing. I’ll try to explain: the agreement was signed by the Civic Coalition, the New Left, the Polish People’s Party, and Poland 2050; thus, there are 4 "portions" of mandates. The Civic Coalition will divide one of those "portions" among its members—Civic Poatform, Modern, Polish Initiative, and The Greens. The Left, however, will share its "portion" with other members of The Left—Left Together, Polish Socialist Party, and Labour Union. Polish People’s Party, similarly, will share its "portion" between the rest of the Polish Coalition. Poland 2050 has the final "portion". The Yes! For Poland will recommend candidates as well, but they’ll get a "place" from either the Civic Coalition’s, or Polish People’s Party’s "portion". So, I wanted to bold those who gained their own "portions" of candidates/mandates. There will be 100 candidates in total, one for each electoral district; the "portion" then de facto means a number of districts. I’m not sure why they just didn’t give "portions" to the Civic Coalition, The Left, the Polish Coalition, Poland 2050, and the Yes! For Poland, but that’s how the agreement has been concluded. TaurenMoonlighting (talk) 20:30, 21 March 2023 (UTC)
I’ve edited the infobox’s Pact members section, and it should be OK for now. If you find some time, could you have a look at the article’s citation formatting and its consistency, please? I feel some of the refs have random titles, but I’m not an expert. Thank you for the help, I appreciate it! Regards, TaurenMoonlighting (talk) 02:38, 22 March 2023 (UTC) EDIT: You did a great job! I’ve corrected ref 3; is it OK now?
Thank you so much for your help, your efforts are much appreciated! Regarding ref 3, "Wyborcza" is the name of a Polish daily newspaper; Gazeta Wyborcza (lit. The Electoral Gazette, or "Election Newspaper"; both names have been used on English Wikipedia). It is commonly referred to as simply Wyborcza, and thus I wonder how should it be translated to English: (The) Electoral (perhaps simply Electoral), or Election? I hope you don’t mind I messaged you. Cheers, TaurenMoonlighting (talk) 14:16, 24 March 2023 (UTC)

Not certain about translations. I don't know Polish and I am relying on Google Translate. Concerning how to cite Wyborcza, why not include both |work= and |trans-work=? Cheers. Boghog (talk) 14:44, 24 March 2023 (UTC)

WP:MolBio button

Hi Boghog, could I ask you to tast whether the "participate" button on Wikipedia:WikiProject Molecular Biology works? I've been wondering why so few ppl have signed up and whether it's because the button is unfamiliar, or if the module is actuall broken! Thanks - T.Shafee(Evo&Evo)talk 01:49, 3 April 2023 (UTC)

Hi Evo! I tried adding myself as a member, but it did not seem to work. So it appears that the module is broken. Cheers. Boghog (talk) 03:54, 3 April 2023 (UTC)
I noticed that User:Boghog/WikiProjectCards/WikiProject Molecular Biology was created, but the link to Wikipedia:WikiProject Molecular Biology/Members was not. Boghog (talk) 04:06, 3 April 2023 (UTC)

Proteinoid

Hi Boghog! I hope you’re having a great Easter weekend. I’d like to expand the article Proteinoid, but have some problem with wording etc. In 1994, Pappelis and Fox proposed a taxonomic category for all proteinoid microspheres—Domain, or Kingdom Protolife. In addition, it includes a certain kind of proteinoid microsphere protocells, capable of synthesizing ATP, polynucleotides and polipeptides—"metaprotocells". The source: http://www2.asa3.org/archive/evolution/199907/0062.html Could you add this information to the article, please? It has been requested by someone on its talk page as well. I believe two or three sentences would be enough, simply to let readers know about that. https://link.springer.com/chapter/10.1007/978-94-011-5056-9_26 Thank you! TaurenMoonlighting (talk) 10:25, 9 April 2023 (UTC)

Hi TaurenMoonlighting, likewise, I hope that you are enjoying the Easter weekend. I had a quick look at the source that you mentioned and added them as further reading in Proteinoid. In short, remarkable claims require remarkable evidence. Per WP:SECONDARY, secondary source (review articles) are strongly preferred, and especially in cases like these. Concerning PMID 34561428 which was mentioned on the Talk:Proteinoid pages, Google Scholar lists 27 sources that have cited PMID 34561428. I really don't have a lot of time to look into this at the moment. In the Google Scholar link above, can you identify any review articles that provide an up-to-date analyis of the field? Cheers. Boghog (talk) 13:20, 9 April 2023 (UTC)
Thanks very much for your help, I appreciate it! Since the article isn’t open access, would it be possible to add a brief note for readers, e.g. - On a proposed taxonomic category that encompasses all the types of proteinoid microspheres, or something like that? I don’t know how it works on Wikipedia, but I’ve found such a suggestion at Wikipedia:Further reading. TaurenMoonlighting (talk) 16:48, 9 April 2023 (UTC)

Model lipid bilayer

Hi Boghog! It's been a while, I hope you're doing well. I wanted to add the following reference to the mentioned article, but I don't know if it'd be possible to use it as a cite (e.g. in the lead), or perhaps it should be placed at Further reading? Cheers, Jojnee (talk) 14:30, 16 April 2023 (UTC)

Hi Jojnee. The citation that you mention:
is probably more suited to Abiogenesis than Model lipid bilayer. It could easily be added as a further reading citation. Normally there should not be anything in the lead that is not discussed in more detail in the body of the article. I think the citation would fit naturally in the Abiogenesis#Producing_suitable_vesicles section. Cheers. Boghog (talk) 16:21, 16 April 2023 (UTC)

New Page Patrol – May 2023 Backlog Drive

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MediaWiki message delivery (talk) 17:11, 20 April 2023 (UTC)

Lamotrigine citation

Hello Boghog. Yesterday, I added a section on the chemistry of lamotrigine. I use the WP:Citation expander in my sandbox to draft most of my technical content using {{cite journal}} and DOI for the cites and when the preview looks correct I copy/paste the addition into the relevant article. I know that you regularly use a bot to convert citations to Vancouver style and I also know that not all editors think your changes are an improvement. I'm not too fussed by that, in general. However, in this edit your bot changed one of the citations so that the link to a freely-available .pdf was removed (its URL is not equivalent to the DOI's target). That seems to me to be a disservice to readers. I suggest you modify the bot to retain that type of link. Mike Turnbull (talk) 21:59, 22 April 2023 (UTC)

Sorry about that. The problem is that {{cite journal}} assumes that the URL points to an open source, where as many times it isn't. The tools that include |url= aren't checking the status of the URL and are not adding |url-access=subscription when appropriate. As you point out, in this case the URL pointed freely available content and hence I have restored that URL. What I will do is change the script so that it only removes URLs that are on a black list (e.g., www.sciencedirect.com). This is a more conservative approach that should minimize the removal of open source URLs. Boghog (talk) 11:17, 23 April 2023 (UTC)

ZXDC

Hi Boghog, can you let me know why you are removing my information for ZXDC protein? CsumbFB (talk) 21:09, 27 April 2023 (UTC)

Hi @CsumbFB: Thanks for your contributions. The reasons for the removal were explained in my edit summaries:
  • diff removed redundant facts section; some of this material has been moved to other sections; none of it was sourced; also the whole article is filled with facts; makes no sense to have a separate facts section
  • diff Wikipedia article's do not have summary sections; they have leads that summarize the entire article
  • diff removed unsourced speculation (see WP:OR)
I hope this makes sense. Cheers. Boghog (talk) 21:59, 27 April 2023 (UTC)

For your help with cleaning up citations on Triage

My fellow Wisconsinite, For helping with my improvements to the Triage page, I grant you a plenary indulgence. Foxtrot620 (talk) 18:48, 10 May 2023 (UTC)
Thank you Foxtrot! Cheers. Boghog (talk) 15:15, 11 May 2023 (UTC)

Hello boghoc how are you?😊 I hope your fine😁☺️

However, I made some sources research

[1] this source says that 12,5 mg IM all three weeks equals 10 mg oral fluphenazine per day which is roughly calculated a 14 fold potentiation in strengh, so in this source its even 11 fold Higher as I said[2] so first I must say I was wrong the 2-3 fold potentiation was for the HCL version, but this source says that the absolute highest dose recommended for the deaconate Version is 100mg for four weeks which at least equals 50 mg oral fluphenazine which is (If the doctors stick to therecommended doses) at least one of the highest values in potency currently on the market since the maximum recommended Dose of haloperidol was decreased to 20 mg per day. Materie34 (talk) 18:28, 23 May 2023 (UTC)

Hi @Materie34:. Thank you for your contributions. The main reason that I undid your edit is that you did not provide any sources. Above you provided sources which is highly appreciated. A second reason is the dosage information is probably too detailed for drug article in Wikipedia. Per WP:PHARMOS, Do not include dose or titration information except when they are extensively discussed by secondary sources, necessary for the discussion in the article, or when listing equivalent doses between different pharmaceuticals. Does this make sense? Cheers. Boghog (talk) 19:27, 23 May 2023 (UTC)
ok thank you for your answer😊 Materie34 (talk) 11:34, 24 May 2023 (UTC)

References

  1. ^ "fluphenazine (Rx)". MedScape. WebMD LLC.
  2. ^ "Fluphenazine Dosage". MedScape. WebMD LLC.

Hei boghoc🙂❤️

I Just wanted to say, that I made a Long entry at the perphenazine site. Its the first editing since my fluphenazine edit, so since a month. I really don't want to make troubles for you as Wikipedia experts so I try to edit very rarely. It it makes so much fun to me 😁 but for sure I am an Amateur so I contacted you and the user verytas 😊 I Wish you a great Weekend, bye😊❤️ Materie34 (talk) 23:11, 22 June 2023 (UTC)

New pages patrol needs your help!

New pages awaiting review as of June 30th, 2023.

Hello Boghog,

The New Page Patrol team is sending you this impromptu message to inform you of a steeply rising backlog of articles needing review. If you have any extra time to spare, please consider reviewing one or two articles each day to help lower the backlog. You can start reviewing by visiting Special:NewPagesFeed. Thank you very much for your help.

Reminders:

Sent by Zippybonzo using MediaWiki message delivery at 06:58, 1 July 2023 (UTC)

TAS2R14 page

Dear editor, once in 2 years I teach a course in which students can chose a wikipedia page to edit as their final project. Two years ago, TAS2R14 page was extended in this manner. This year, another student was working on this page. Most of his changes were not accepted, but what is surprising to me that some of the older content was deleted as well. So now this page no longer has information on known ligands, known SNPs and mutations, or lacks links to recent papers. Your help is appreciated. https://wiki.riteme.site/wiki/TAS2R14 128.139.19.124 (talk) 09:13, 24 July 2023 (UTC)

Hi. No problem. Previous versions are never completely deleted, just archived. Click the history tab on the article, select a earlier version, clik edit, and copy the raw text. Cheers. Boghog (talk) 09:31, 24 July 2023 (UTC)

An automated process has detected that when you recently edited List of proteins, you added a link pointing to the disambiguation page EC number.

(Opt-out instructions.) --DPL bot (talk) 06:03, 26 July 2023 (UTC)

Since you do a lot of citation work...

These pieces might interest you. Headbomb {t · c · p · b} 17:50, 1 August 2023 (UTC)

Citation Help

Hi BogHog,

I'm having a bit of trouble citing one of my sources on my page of Obturator hernia, can you take a look at it? Thank you! Immanueltjahjadi (talk) 21:56, 1 August 2023 (UTC)

Hi Immanueltjahjadi. Thank you for your contributions to the Obturator hernia. I am not certain which reference you are referring to. Did you mean Schizas 2021? Since that source was already cited and was already had a ref name "Schizas_2021", you just need to insert the tag <ref name = "Schizas_2021" /> to the location you want to recite Schizas 2021 (see WP:REFNAME). Cheers. Boghog (talk) 04:25, 2 August 2023 (UTC)

HGNC-UNIPROT ID pairs in the HGNC database and Wikidata

Hey Boghog,

I took a look at how I might create a combined dataset from the HGNC protein-coding gene file & Wikidata's gene & protein data items. In a nutshell, I need to run a SPARQL query on Wikidata (or alternatively, on UNIPROT) with the mkwikidata library to pull more information on the gene and/or protein than what is listed in the current data file my bot uses. From there, I can just use pandas to merge the two datasets on HGNC-UNIPROT ID pairs and write the merged dataset to a tab-delimited file with that same formatting as the current "protein-coding gene.txt" file my bot uses. Not a problem to merge the two, although it appears there will be a few cases where HGNC-UNIPROT ID pairs in one dataset aren't matched to the same ID pair in the other.

Based on an initial look, there are a lot more HGNC-UNIPROT pairs listed in wikidata than in the HGNC "protein-coding gene.txt" file. That's not really a problem. I was planning on dropping any HGNC-UNIPROT ID pairs from Wikidata that aren't paired in the HGNC's dataset, so the extra ID pairs present in Wikidata won't pose an issue.

It's sort of a problem if the HGNC-UNIPROT ID links in the HGNC file aren't matched in Wikidata because it will render in the wikitables as partially blank rows for any entries with unpaired HGNC-UNIPROT IDs in Wikidata (i.e., the gene symbol, HGNC ID, and UNIPROT ID from the HGNC file will still appear in a table row for that HGNC-UNIPROT ID pair, but any columns of information I pull from Wikidata for that HGNC-UNIPROT ID pair will contain missing data). There are only 40 genes with more than one Uniprot ID in the HGNC's "protein-coding gene.txt" file, and they only contribute a total of 82 unique HGNC-UNIPROT ID pairs (NB: these are all listed in collapse tab below). So, while I don't think this is likely to be a prevalent issue, I did find one instance of wikidata missing an ID pair that's present in the HGNC dataset. E.g., from special:permalink/1166507817 in row #14387 SCRIB has the following HGNC-UNIPROT ID pairs:

I'm not sure if the first HGNC-UNIPROT pair actually should be listed in Wikidata or not after looking at UNIPROT and HGNC separately. I was wondering if you knew why they aren't.


HGNC IDs that are linked to more than one UNIPROT ID in the "protein-coding gene.txt" file

For context, the current list of human protein-coding genes contains 19247 HGNC IDs and 19289 HGNC-UNIPROT ID pairs. I need to use the pair of identifiers to perform a 1:1 merge of the gene-protein entries in HGNC & Wikidata datasets or HGNC & Uniprot datasets simply because HGNC ID & UNIPROT ID have a one-to-many relationship on this tiny portion of the HGNC dataset.

HGNC:377 Uniprot links: O43687, Q9P0M2
HGNC:17868 Uniprot links: Q96PG8, Q9BXH1
HGNC:1437 Uniprot links: P01258, P06881
HGNC:1787 Uniprot links: P42771, Q8N726
HGNC:24346 Uniprot links: Q96RT6, Q9HC47
HGNC:2557 Uniprot links: P39880, Q13948
HGNC:2726 Uniprot links: P0DPQ6, P35638
HGNC:19681 Uniprot links: Q6B8I1, Q9UII6
HGNC:3413 Uniprot links: B3EWF7, O95278
HGNC:3438 Uniprot links: P0DP91, Q03468
HGNC:4392 Uniprot links: O95467, P63092, P84996, Q5JWF2
HGNC:23037 Uniprot links: A8MTL9, P0C7T4
HGNC:13664 Uniprot links: O94854, Q9UPN3
HGNC:25979 Uniprot links: L0R8F8, Q9NQG6
HGNC:7193 Uniprot links: O96007, O96033
HGNC:31104 Uniprot links: O95411, Q92614
HGNC:7629 Uniprot links: E9PAV3, Q13765
HGNC:8008 Uniprot links: P58400, Q9ULB1
HGNC:8009 Uniprot links: P58401, Q9P2S2
HGNC:8010 Uniprot links: Q9HDB5, Q9Y4C0
HGNC:20422 Uniprot links: P0DPB5, P0DPB6
HGNC:14862 Uniprot links: P0CAP2, Q6EEV4
HGNC:9403 Uniprot links: C0HM02, P24723
HGNC:9449 Uniprot links: F7VJQ1, P04156
HGNC:16519 Uniprot links: P0DI83, Q9BZG1
HGNC:24663 Uniprot links: B7ZAP0, Q5R372
HGNC:9896 Uniprot links: P0DW28, P98175
HGNC:2569 Uniprot links: A6ZKI3, O15255
HGNC:30377 Uniprot links: C0HLS1, Q14160
HGNC:10845 Uniprot links: P60896, Q6ZVN7
HGNC:15928 Uniprot links: O00241, Q5TFQ8
HGNC:20753 Uniprot links: L0R6Q1, Q96G79
HGNC:11875 Uniprot links: P42166, P42167
HGNC:24055 Uniprot links: Q8NFQ8, Q9H496
HGNC:11996 Uniprot links: Q5JU69, Q8N2E6
HGNC:12027 Uniprot links: P0DSE1, P0DTU3
HGNC:12155 Uniprot links: P0DSE2, P0DTU4
HGNC:1158 Uniprot links: B1AH88, P30536
HGNC:18194 Uniprot links: Q70YC4, Q70YC5
HGNC:25173 Uniprot links: C0HLU2, Q96CS4


Also, SPARQL is fairly new to me. I'm pretty sure, but not 100% certain, that this query yields all the relevant HGNC-UNIPROT ID pairs for human protein-coding genes on Wikidata. I need to read more about SPARQL queries and look at the descriptive statistics for this dataset in Python to be sure. I imagine a Wikidata project might be able to help me out too, though. 

SELECT DISTINCT ?gene ?geneLabel ?HGNC_ID ?HGNCsymbol ?protein ?proteinLabel ?UNIPROT_ID ?wd_gene_item_article_link ?wd_protein_item_article_link
 {
   ?gene wdt:P31 wd:Q7187 .
   ?gene wdt:P703 wd:Q15978631 .
   ?gene wdt:P279 wd:Q20747295 .
   ?gene wdt:P354 ?HGNC_ID .
   ?gene wdt:P353 ?HGNCsymbol .
   ?gene wdt:P688 ?protein .
   ?protein wdt:P352 ?UNIPROT_ID .
    OPTIONAL { 
    ?article 	schema:about ?gene ;
                schema:name ?wd_gene_item_article_link ;
 			    schema:isPartOf <https://wiki.riteme.site/> .
    }
    OPTIONAL { 
    ?article 	schema:about ?protein ;
                schema:name ?wd_protein_item_article_link ;
 			    schema:isPartOf <https://wiki.riteme.site/> .
    }
   SERVICE wikibase:label { bd:serviceParam wikibase:language "en" } .
 }

Click here to launch the Wikidata query

Seppi333 (Insert 2¢) 18:54, 26 July 2023 (UTC)

Hi Seppi333. This is really cool! I am impressed that you were able to do this so quickly. I don't have any experience with SPARQL either, but it looks pretty powerful. I didn't realize that there is one to many relationship between HGNC and UniProt IDs. I was under the impression that various splice variants of a gene would be listed under a single UniProt entry, but apparently not always the case. Concerning unmatched HGNC/UniProtpairs, these look to be rare, so I would think that these are simply an uncorrected errors. So it looks like it will be straight forward to add extra columns to your list, assuming that there is consensus to do so. We need for the AfD to close and then decide what to do. Thanks for your help! Cheers. Boghog (talk) 19:14, 26 July 2023 (UTC)
No worries. Main reason I did this was out of curiosity; I just wanted to see how feasible it is to perform a dataset merger using matched gene-protein identifiers in two different databases. On the off-chance that a consensus to merge the lists or expand my list occurs, I can expand the SPARQL query to return other data items that are linked to each HGNC-UNIPROT ID pair, like "expressed in" for the linked gene and "molecular function", "cell component", "biological process" for the linked protein. Seppi333 (Insert 2¢) 19:46, 26 July 2023 (UTC)
After looking more into this, it looks like my problem is a solution to another problem. Probably going to need to create a data pipeline from HGNC to Wikidata and get a Wikidata bot approved to add missing HGNC-UNIPROT ID links in Wikidata from the HGNC dataset prior to running a script that queries Wikidata and merges the returned dataset with the HGNC data.
Also, I used a slightly modified version of the query above to find proteins without UNIPROT IDs that are linked to HGNC IDs. After quickly skimming the 400 or so additional proteins the query returned, I noticed EAAT3 (Q11856447) was missing a UNIPROT ID, which I thought was odd considering that I'm familiar with the gene and protein. The UNIPROT ID is already linked to SLC1A1 (Q18031520), and I don't even need to look at a database to know these are duplicate Wikidata entries. I probably ought to generate dataset of HGNC IDs that are linked to two or more proteins where at least one protein is missing a UNIPROT ID to find duplication issues in Wikidata like this one. Would need to be manually checked, but it should be fairly manageable (less than 1000 entries). For now, it's probably best to let this duplicate entry remain unmerged so that I know whatever SPARQL query I write to locate duplicate entries actually finds that true positive case.
#title: Sort on the UNIPROT_ID column to see the ~400 proteins linked to an HGNC ID that are missing a UNIPROT identifier.
SELECT ?gene ?geneLabel ?HGNC_ID ?HGNCsymbol ?protein ?proteinLabel ?UNIPROT_ID ?wd_gene_item_article_link ?wd_protein_item_article_link
 {
   ?gene wdt:P31 wd:Q7187 .
   ?gene wdt:P703 wd:Q15978631 .
   ?gene wdt:P279 wd:Q20747295 .
   ?gene wdt:P354 ?HGNC_ID .
   ?gene wdt:P353 ?HGNCsymbol .
   ?gene wdt:P688 ?protein .
    OPTIONAL {
    ?protein wdt:P352 ?UNIPROT_ID .
    }
    OPTIONAL { 
    ?article 	schema:about ?gene ;
                schema:name ?wd_gene_item_article_link ;
 			    schema:isPartOf <https://wiki.riteme.site/> .
    }
    OPTIONAL { 
    ?article 	schema:about ?protein ;
                schema:name ?wd_protein_item_article_link ;
 			    schema:isPartOf <https://wiki.riteme.site/> .
    }
   SERVICE wikibase:label { bd:serviceParam wikibase:language "en" } .
 }

Click here to launch the Wikidata query

First it was a mountain of DABlinks on Wikipedia. Now it's this. I always seem to find tons of stuff that needs to be fixed whenever I do any work involving my bot script... lol.
In any event, I'll bring this up at Wikidata:Wikidata:WikiProject Molecular biology once I do a little more work on this. Seppi333 (Insert 2¢) 02:47, 28 July 2023 (UTC)
So… looks like the consensus was to draftify. I could reopen the original RFBA to generate consensus. Was wondering if you think others might support revising the lists. I don’t mind doing the programming work, but I don’t really want to unilaterally attempt to convince everyone for bot approval like last time. Seppi333 (Insert 2¢) 17:32, 3 August 2023 (UTC)
@Seppi333: Hi Seppi. The creater of the list, Claes Lindhardt, asked How do I update my vote to Merge?. I interpret that comment as there is support to expand your list by merging. But what is meant by merge? We can merge by columns or rows. I think merging by columns make a lot more sense since the required data can be downloaded from reliable web sources. For such a huge list, human generated content is not practical. The target articles are a much more logical place to put human generated content. The question then becomes is what columns to add. Boghog (talk) 18:02, 3 August 2023 (UTC)
PS: How did you pick up SPARQL so quickly? I have a use case in real life to write UniProt SPARQL queries. Do you have any recommendations for learning SPARQL? Learning SPARQL look promising. Boghog (talk) 18:02, 3 August 2023 (UTC)
Eh, I’m not really that inclined to make the lists editable, if that’s what you meant. I suppose I could try reopening the RDBA in about 2 weeks when I’ll have more time to focus on this.
As for SPARQL, I just picked it up from looking at example syntax and through trial and error. It’s my first query language, but a lot of people tell me I’m a really fast learner, so IDK if that approach works the same for everyone. Seppi333 (Insert 2¢) 20:46, 3 August 2023 (UTC)
@Seppi333: I’m not really that inclined to make the lists editable I complety agree with you, that would be an incredibly bad idea. There is no need to re-invent the wheel. Just download the data from HUGO and UniProt. Boghog (talk) 20:56, 3 August 2023 (UTC)

ALS Good Article Nomination

Hey there wiki-buddy! I'm hoping I can attract some interested folks to consider reviewing the Wikipedia page about amyotrophic lateral sclerosis for Good Article status. As you may know, ALS is a rare and fatal neurodegenerative disease that quickly causes people to lose the ability to move, speak, and breathe. The Wikipedia page about ALS is read over 2,000 times each day in English alone, and often experiences spikes in traffic whenever a celebrity is diagnosed. There have recently been a number of genetic advances made in the space and some recent drug approvals, thanks in part to the momentum started by the ALS Ice Bucket Challenge. I've been grinding away at it since early this year but keen to see it improve further, hope you'll consider! PaulWicks (talk) 08:38, 6 August 2023 (UTC)

Good article reassessment for Osteopathic medicine in the United States

Osteopathic medicine in the United States has been nominated for a good article reassessment. If you are interested in the discussion, please participate by adding your comments to the reassessment page. If concerns are not addressed during the review period, the good article status may be removed from the article. ~~ AirshipJungleman29 (talk) 15:55, 8 August 2023 (UTC)

Category:Genes on human chromosome has been nominated for merging

Category:Genes on human chromosome has been nominated for merging. A discussion is taking place to decide whether this proposal complies with the categorization guidelines. If you would like to participate in the discussion, you are invited to add your comments at the category's entry on the categories for discussion page. Thank you. Gjs238 (talk) 22:44, 15 August 2023 (UTC)

Tandem repeat

Hi Boghog, the article Tandem repeat seems to be missing some substantive content. Shouldn't satDNA be at least briefly described there (e.g. in the Terminology section)? Cf. Satellite DNA. TaurenMoonlighting (talk) 22:00, 28 August 2023 (UTC)

I am not an expert in this area. Please be WP:bold and expand the article if you think it is incomplete. Cheers. Boghog (talk) 03:38, 29 August 2023 (UTC)

New page patrol October 2023 Backlog drive

New Page Patrol | October 2023 Backlog Drive
  • On 1 October, a one-month backlog drive for New Page Patrol will begin.
  • Barnstars will be awarded based on the number of articles and redirects patrolled.
  • Barnstars will also be granted for re-reviewing articles previously reviewed by other patrollers during the drive.
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MediaWiki message delivery (talk) 09:13, 9 September 2023 (UTC)

New pages patrol newsletter

Hello Boghog,

New Page Review article queue, March to September 2023

Backlog update: At the time of this message, there are 11,300 articles and 15,600 redirects awaiting review. This is the highest backlog in a long time. Please help out by doing additional reviews!

October backlog elimination drive: A one-month backlog drive for October will start in one week! Barnstars will be awarded based on the number of articles and redirects patrolled. Articles will earn 4x as many points compared to redirects. You can sign up here.

PageTriage code upgrades: Upgrades to the PageTriage code, initiated by the NPP open letter in 2022 and actioned by the WMF Moderator Tools Team in 2023, are ongoing. More information can be found here. As part of this work, the Special:NewPagesFeed now has a new version in beta! The update leaves the NewPagesFeed appearance and function mostly identical to the old one, but updates the underlying code, making it easier to maintain and helping make sure the extension is not decommissioned due to maintenance issues in the future. You can try out the new Special:NewPagesFeed here - it will replace the current version soon.

Notability tip: Professors can meet WP:PROF #1 by having their academic papers be widely cited by their peers. When reviewing professor articles, it is a good idea to find their Google Scholar or Scopus profile and take a look at their h-index and number of citations. As a very rough rule of thumb, for most fields, articles on people with a h-index of twenty or more, a first-authored paper with more than a thousand citations, or multiple papers each with more than a hundred citations are likely to be kept at AfD.

Reviewing tip: If you would like like a second opinion on your reviews or simply want another new page reviewer by your side when patrolling, we recommend pair reviewing! This is where two reviewers use Discord voice chat and screen sharing to communicate with each other while reviewing the same article simultaneously. This is a great way to learn and transfer knowledge.

Reminders:

MediaWiki message delivery (talk) 16:45, 22 September 2023 (UTC)

Your edits on psychiatry articles

The above edits of yours seem completely incorrect. Many citations are incorrectly replaced with "Transcriptional profiling of lung cell populations in idiopathic pulmonary arterial hypertension". 133.106.241.155 (talk) 09:19, 14 October 2023 (UTC)

Thanks for your message. The above edits were mostly correct but a few of the citations were incorrectly substituted. There was a bug is a script that I was using. The problem is that PubMed has recently started returning close matches for DOI searches. I have done additional checks for the citations and the script no longer makes this particular error. Boghog (talk) 11:52, 14 October 2023 (UTC)

Edit the author names automatically

Hello, do you have a tool to edit the author names automatically? Can you please replace all names to "vauthors" in all references at Androgen backdoor pathway? Thank you in advance! --Maxim Masiutin (talk) 12:55, 19 October 2023 (UTC)

Thank you for your contributions! I have a script that standardized names based on citation data pulled from PubMed. Per your request, substituted first, last, ... with vauthors. Cheers. Boghog (talk) 18:23, 19 October 2023 (UTC)
Thank you! If you will occasionally check for substance the pages (sections) that I edit, I'd be grateful! --Maxim Masiutin (talk) 19:54, 19 October 2023 (UTC)

Changing established citation style

Boghog, sorry to trouble you, but I'm almost sure I mentioned to you a long while back that you - anybody - must not change established citation style in any article, as that is forbidden by policy. I have over the years reverted quite a number of such changes that you had made, sometimes at a considerable cost in time and effort, and I had supposed you had stopped doing this, at least in areas like evolutionary biology where I often edit. However this edit was made only last month. The behaviour is unacceptable and must stop immediately. If you have made any more edits like that recently, I'd be much obliged if you could undo them. Please don't ever do this again. Many thanks! Chiswick Chap (talk) 18:51, 22 October 2023 (UTC)

Just a suggestion. If you want to convert the author style, just deleted the |vauthors= parameter and run Citation bot which will repopulate with |last1=, |first1=. This will be much less work for you and also preserve other edits to the citations. For example, in Excavata I had updated a citation to a preprint with the full journal citation which was overwritten. Also I note that before my edits, Excavata had a mix of citations styles (first initials vs. spelled out first author names, and |author1= vs. |last1=, |first1=). After this edit, they should be completely consistent. Boghog (talk) 04:13, 23 October 2023 (UTC)

November Articles for creation backlog drive

Hello Boghog:

WikiProject Articles for creation is holding a month long Backlog Drive!
The goal of this drive is to reduce the backlog of unreviewed drafts to less than 2 months outstanding reviews from the current 4+ months. Bonus points will be given for reviewing drafts that have been waiting more than 30 days. The drive is running from 1 November 2023 through 30 November 2023.

You may find Category:AfC pending submissions by age or other categories and sorting helpful.

Barnstars will be given out as awards at the end of the drive.

There is a backlog of over 1800 pages, so start reviewing drafts. We're looking forward to your help! MediaWiki message delivery (talk) 13:23, 31 October 2023 (UTC)

Edit four steroid pages for consistent citation formatting (use vauthors instead of firstN/lastN)

Hello!

Could you please use your script to edit four steroid pages for consistent citation formatting (use vauthors instead of firstN/lastN). There are too many firstN/lastN that I could not edit them manually. Here are the pages:

  1. Dihydrotestosterone
  2. 5α-Pregnan-17α-ol-3,20-dione
  3. 5α-Pregnane-3α,17α-diol-20-one
  4. Progesterone

Also, could you please consider publishing your script to the tools-forge in addition to your great "Wikipedia template filling" script. I use it, thank you very much!

-- Maxim Masiutin (talk) 20:24, 20 October 2023 (UTC)

@Boghog: Can you please also process Congenital adrenal hyperplasia due to 21-hydroxylase deficiency to replace citations to "vauthors" where they are not so? Thank you in advance! --Maxim Masiutin (talk) 21:20, 3 November 2023 (UTC)

Help

Can you help with the ref section of this article?


Colonoscopy


I tried to update them - I have no real clue - any help would be appreciated - BeingObjective (talk) 05:19, 10 November 2023 (UTC)

Many thanks - I noticed you worked some magic. BeingObjective (talk) 13:18, 10 November 2023 (UTC)

Making the consistent citation tool available by online request

Would you please consider making your consistent citation tool available by online request, like you did with Wikipedia template filling, at least to a beta tester like me? 😊 Maxim Masiutin (talk) 08:45, 12 November 2023 (UTC)

Hi. The script is buggy and has turned into a rats nest of code. Right now, it only pulls data from PubMed, but I would like to add other sources of data like Google Scholar and WorldCat. The script really needs to be rewritten from scratch. I don't have time to do this now, but perhaps over the holidays. Then perhaps it could be made avaiable as an on-line tool. Cheers. Boghog (talk) 08:54, 12 November 2023 (UTC)

Many thanks for your citation assist.

Just a thank you - I noted the clean ups of my messes reg. citations.

As a newbie - I thought you were a bot.


Apologies.


BeingObjective (talk) 22:27, 23 November 2023 (UTC)

@BeingObjective - can you please post here a diff where the change was incorrect, so @Boghog could improve the script?
@Boghog: Can you please share the script on Github so I could improve it to support cite template and atributes on other languages since I edit different languages of Wikipedia. Maxim Masiutin (talk) 22:41, 23 November 2023 (UTC)

CYP4F2

Hello! When you have time, please let me know what you think on CYP4F2 article? I expanded it based on the reference on WP:MCBMOS that you provided. How can I further improve the article, or fix the omissions or errors that you may find and tell me about? Maxim Masiutin (talk) 05:02, 25 November 2023 (UTC)

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Feeback on an illustration for HNMT

Hello! I made an illustration for HNMT that shows a chemical reaction. Is such a kind of illustration OK for Wikipedia? Maxim Masiutin (talk) 20:20, 28 November 2023 (UTC)

File:HNMT-methylation-of-histamine.svg looks OK to me. A couple of minor requests. For simplicity, I think all the color ovals should be transparent. Mixing solid and tranparent is a bit confusing. Also the emphasis should be on histamine hence cosubstrates should be moved closer together and under the reaction arrow. Cheers. Boghog (talk) 20:34, 28 November 2023 (UTC)
OK, than you! Will try to rearrange! Maxim Masiutin (talk) 20:40, 28 November 2023 (UTC)
That definitely is an improvement. Thanks. Boghog (talk) 03:31, 29 November 2023 (UTC)

Send me an email please

Hello! Could you please send me an email via Wikipedia, I will reply via email to avoid discussing on the User Talk page. Thank you very much for considering my request! Maxim Masiutin (talk) 12:48, 30 November 2023 (UTC)

Vancouver Initials of longer than 2 characters

When using the Template Filing Tool to expand a PubMed ID, it sometimes generates the vauthors string with initials consisting of more than 2 characters which is reported as error in the references list on Wikipeidia when I insert the reference. For example, John AB. "Title". Journal. is ok, but it can sometimes generate John A. "Title". Journal. {{cite journal}}: Vancouver style error: initials in name 1 (help) which gives the "Vancouver style error: initials in name 1" error". Can you please update the citation template filling tool? Maxim Masiutin (talk) 20:14, 2 December 2023 (UTC)

Hi. The tool was written by User:Diberri. I just try to keep it up and running. I will see if I can hack the script to restict the author initials to two characters. Cheers. Boghog (talk) 20:26, 2 December 2023 (UTC)
(talk page stalker) @Maxim Masiutin: I think you can find the source code for this tool at https://metacpan.org/dist/WWW-Wikipedia-TemplateFiller see https://metacpan.org/author/DIBERRI for more info. --WikiLinuz (talk) 06:58, 3 December 2023 (UTC)
Do you have a specific example (e.g., a |pmid= that has an author with more than two characters for first initials)? I need an example for testing. I have added the following code to the template filler script which shoud take care of it (dislaimer: I very rarely code in perl), but I have not tested with an example with more than two characters in the first initials.
# limit first initials to two characters as this is all vauthors will accept
  while (my ($ArrayIndex, $ArrayItem) = each @authors) {
    my @spl = split(' ', $authors[$ArrayIndex]);
    if (scalar(@spl) > 1) {
      $spl[-1] = substr( $spl[-1], 0, 2);
      $authors[$ArrayIndex] = join ( ' ', @spl );
    }
  }

Boghog (talk) 17:28, 3 December 2023 (UTC)

Thank you, it took me a while to find an example, because they happen here and there, but I forgot to note. I found one at PMID 31463682, see Zorzella-Pezavento SFG - diff from a page with the real-life example Maxim Masiutin (talk) 17:51, 3 December 2023 (UTC)
I've checked now, and it is OK, thank you very much! Maxim Masiutin (talk) 17:51, 3 December 2023 (UTC)

RefRenamer

I see that you are using the RefRenamer tool. It did not support "pmid" to create named references by this attribute automatically, but I added support for that and other attributes, in my local copy of the script and asked the author to consider supporting that in the main instance. Maxim Masiutin (talk) 20:49, 3 December 2023 (UTC)

Good idea. Thanks. Boghog (talk) 04:36, 4 December 2023 (UTC)
After the discussion with the author I removed all attributes that I added except "pmid" because the reference names have to have semantic meaning (when people may refer to them), and they have such only for pmid. Maxim Masiutin (talk) 04:38, 4 December 2023 (UTC)

Name list style template

Do you think we should introduce a Name list style template similar to that of date format template {{Use mdy dates}}

We can introduce something like {{Use vanc name-list-style}}

And we also implement changes to https://github.com/ms609/citation-bot so that if the bot sees that template, the bot will use that format, and you will not need to use your script over and over again? Maxim Masiutin (talk) 01:36, 6 December 2023 (UTC)

I submitted a pull request for the citation bot: https://github.com/ms609/citation-bot/pull/4236
I also want to implement a template to denote reference style "pmidNNNNN", i.e. whenever a there is a template such as , then if a reference has a |pmid=" attribute, then it it should be named as "pmidNNNNN". This is useful for bots that can put names and to avoid style wars. Other references that do not have a pmid may have any name, this template should only be for those that have PMID. Maxim Masiutin (talk) 04:42, 6 December 2023 (UTC)
The already works in this bot. Maxim Masiutin (talk) 04:43, 6 December 2023 (UTC)
{{Use vanc name-list-style}} is an interesting idea, but likely to be highly controversial. It would also need buy-in from the maintainers of User:Citation Bot which is far from guaranteed.
There is also {{cs1 config|name-list-style=vanc|display-authors=6}} which causes {{cite journal}}, etc templates to render authors in Vancouver style. Boghog (talk) 04:58, 6 December 2023 (UTC)
why do you edit each citation when there is such a config template?
the use dmy template is just informational, it doesn't alter how is the page rendered, similar are those templates that I propose Maxim Masiutin (talk) 05:12, 6 December 2023 (UTC)
The reason I edit each refererence is to declutter the raw wiki text from |first1=, |last1= parameters. In addition, the script does other things like adjust dates, page ranges, adds full journal names, completes author lists, etc. I do realize {{dmy}} is purely informational and it takes human editors and/or bots to implement or maintain the date style. Boghog (talk) 05:31, 6 December 2023 (UTC)
the citation bot probably does almost the same (adjusts dates, etc.); it could understand date format but not the name list style. I saw the source code of the bot, and it is very sophisticated. I hope that it will support the vauthors. should it support it, I will let you know. Maxim Masiutin (talk) 05:40, 6 December 2023 (UTC)
Yes, citation bot is very sophisticated and constantly updated. Thanks for requesting this. I hope the maintainers implement it. Cheers. Boghog (talk) 05:43, 6 December 2023 (UTC)
I implemented it in my fork repository and tested it, it works well. The maintainers have to check the code, test it and decide on merit, whether it worth implementing. I submitted a few other changes earlier today, such as an opportunity to specify PubMed API key for higher request rate, or an ability to save processoages to file rather than updating Wikipedia, or ability to specify timeouts easier, and they accepted surprisingly fast, already accepted those. Maxim Masiutin (talk) 05:53, 6 December 2023 (UTC)
I thought you just requested the feature. I now see that you already implemented it in your fork. Wow! This make it far more likely that this feature will be included in the production version. Thank you! Boghog (talk) 06:06, 6 December 2023 (UTC)

Free fatty acid receptor

Hi @Boghog: How goes it? I notice you created this article. I have another editor who has left a message on my talk page, a retired professor, who has updated the article but doesn't know how to place an updated ID box for a new receptor. Would you be able to assist on this? scope_creepTalk 17:55, 12 December 2023 (UTC)

Hi @Joflaher and Scope creep: Done Per your request, an {{infobox protein}} has been added to Free fatty acid receptor 4 in this edit. Cheers. Boghog (talk) 18:54, 12 December 2023 (UTC)
Boghog ((and scope creep), thank you for your help. . joflaher (talk) 20:54, 12 December 2023 (UTC)

GA Review

I have submitted a few articles fog GA, some few months ago, but they do not progress. I even decided to review a few articles myself to clear the backlog so my articles are closer to get reviewed, but it was not a good experience overall. Could you please help me and review an article from those I nominated for GA which upon your overview is most suitable for GA? That would have motivated me to write other articles or improve existing ones if they are not yet OK for GA. I nominate them but they do not move, so I'm at a loss :-) Maxim Masiutin (talk) 16:52, 18 December 2023 (UTC)

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GA Review Request

Hello, @Boghog

I recently noticed your active participation in the GA review for "Selective androgen receptor modulator" at Talk:Selective_androgen_receptor_modulator/GA1, which caught my attention.

As you may have observed, I also provided a few minor suggestions on the same article regarding its definition, classification, and 11-oxyandrogens. You can find these suggestions filtered here: (1) definition; (2) classification; (3) 11-oxyandrogens.

I am reaching out to you because I have submitted several articles as GA nominees that have been awaiting review for quite some time now. While some of them were relisted with more recent dates due to updates and improvements, others have been pending since April 2023. One particular article titled "Androgen backdoor pathway" was nominated in April 2023 but only reviewed in August of the same year, and unfortunately, it did not meet all the GA criteria as determined by the reviewer. However, had the reviewer given me just a couple of days' time to address the trivial issues raised during their evaluation process, it could easily have complied with all GA requirements outlined for a successful nomination. Consequently, I resolved all the omissions and observations made by the reviewer, and resubmitted it once again, waiting patiently yet eagerly for another opportunity.

At present, multiple articles from my submissions are still awaiting review, a total count five. While attempting to mitigate backlog within this category about one month ago by reviewing other articles myself, some of my reviews received criticism from experienced editors, prompting me to cancel them and return to the backlog queue, while other of my reviews passed scrutiny conducted by experienced editors, as they decided to check all reviews that I have done to not let the mistakes which I made in some reviews to be also present in the other reviews. If I cleared the backlog, there would be fewer reviews in the queue so that future reviewers would catch up on my reviews sooner.

I am, however, hesitant to continue conducting further reviews because I lack sufficient experience. While trying to contribute towards reducing backlog within this category about one month ago by reviewing articles myself, I faced some challenges due to my lack of experience in conducting reviews independently. Unfortunately, @RoySmith, who was one of the reviewers who requested second opinion that I provided, threatened me with potential banning or blocking for incompetence related to these reviews and discussions related to reviews. I agree with incompetence, but there are lesser penalties to punish incompetence and prevent its consequences than the indefinite block.

I was already indefinitely blocked in German Wikipedia, and so I do not want to also be blocked in the English Wikipedia, although I also contribute in other languages, such as Russian, Ukrainian and Romanian, but on smaller extent. On German Wikipedia, the admin used the harshest penalty straight away, whereas much lesser penalties could have solved the issue equally well. I didn't even imagine that a small thing could lead to immediate ban. Therefore, I don't want to be banned here as well. My coauthor of peer-reviewed articles has already been banned here on a sex topic (so he quit editing Wikipedia altogether), and my friends from Germany told that they were also either banned on German Wikipedia or stopped contributing because of admins actions they consider inappropriate, and some of them were long-time editors for more than 15 years, their recommendations about me didn't help to lift the block. This block has consequences for English Wikipedia as well, because I was also blocked from Wikipedia Library, however, I asked the library to lift the block, so I can now access the library again.

Therefore, I don't want to be blocked here on English Wikipedia.

Most importantly, though is, finding suitable mentorship or guidance has proven elusive so far. Despite encountering such difficulties, I remain committed to learning various Wikipedia rules, which are scattered and hard to follow, but I am willing to learn and comply in order to improve Wikipedia. I am using Wikipedia as a reader for various information, and as a way of saying thank you, I am also contributing myself as an editor. I also contributed to Citations Bot programming and to RefRenamer programming.

Having said that, I sincerely request your assistance in reviewing at least one of my submitted articles as a GA candidate. Please consider reviewing at least one of my submissions; for example, you can choose an article that aligns conveniently with your own schedule or perhaps select an article that most closely matches established GA criteria. If you identify any omission or areas of improvement during your review process, I would kindly request to give me a day or two days grace period to ensure a thorough resolution before making a final judgment. Thank you very much for considering my request!

Sincerely, Maxim Masiutin (talk) 15:43, 30 December 2023 (UTC)

Hi. Since there is limited banwidth with GANs, I would suggest that you concentrate on one article before moving on to the next. I will see what I can do with Androgen backdoor pathway. I first need to get my head around the science before I would attempt to review it. One thing that is immediately apparent is the figures (File:Backdoor pathways from P4 and 17OHP to DHT with corticosteroid pathways shown as blue arrows.svg and File:Backdoor-11-oxygenated.svg) are way more complicated than they need to be be. Compare with figure 4b in
with a total of 16 intermediates is able to summarize both the classical (lefthand side) and alternative (righthand side) pathways. Rememeber that we are writing for a general audience and therefore these figure need to be kept as simple as possible. I have some background in this area, and even I am overwhelmed by the present figures. I will continue to work on this over the next few days. Cheers. Boghog (talk) 14:09, 31 December 2023 (UTC)
Thank you for your help! I will reply in an article Talk page. You raised an important point which, I think, should be publicly discussed at the Talk page. Maxim Masiutin (talk) 09:32, 1 January 2024 (UTC)
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