User talk:ProteinBoxBot

NOTE: Discussion of the Gene Wiki project generally happens over at Portal:Gene Wiki/Discussion. Notes about the bot itself can be left below.

A discussion is taking place as to whether the article ARG2 (gene) is suitable for inclusion in Wikipedia according to Wikipedia's policies and guidelines or whether it should be deleted.

The article will be discussed at Wikipedia:Articles for deletion/ARG2 (gene) until a consensus is reached, and anyone is welcome to contribute to the discussion. The nomination will explain the policies and guidelines which are of concern. The discussion focuses on high-quality evidence and our policies and guidelines.

Users may edit the article during the discussion, including to improve the article to address concerns raised in the discussion. However, do not remove the article-for-deletion notice from the top of the article. Prof. Squirrel (talk) 16:34, 8 December 2013 (UTC)Reply

A tag has been placed on GPIHBP1 (gene) requesting that it be speedily deleted from Wikipedia. This has been done under section G12 of the criteria for speedy deletion, because the article or image appears to be a clear copyright infringement. This article or image appears to be a direct copy from http://www.ncbi.nlm.nih.gov/gene/338328. For legal reasons, we cannot accept copyrighted text or images borrowed from other web sites or printed material, and as a consequence, your addition will most likely be deleted. You may use external websites as a source of information, but not as a source of sentences. This part is crucial: say it in your own words. Wikipedia takes copyright violations very seriously and persistent violators will be blocked from editing.

If the external website or image belongs to you, and you want to allow Wikipedia to use the text or image — which means allowing other people to modify it — then you must verify that externally by one of the processes explained at Wikipedia:Donating copyrighted materials. If you are not the owner of the external website or image but have permission from that owner, see Wikipedia:Requesting copyright permission. You might want to look at Wikipedia's policies and guidelines for more details, or ask a question here.

If you think this page should not be deleted for this reason, you may contest the nomination by visiting the page and clicking the button labelled "Click here to contest this speedy deletion". This will give you the opportunity to explain why you believe the page should not be deleted. However, be aware that once a page is tagged for speedy deletion, it may be removed without delay. Please do not remove the speedy deletion tag from the page yourself, but do not hesitate to add information in line with Wikipedia's policies and guidelines. Ethically ^(Yours) 12:40, 12 December 2013 (UTC)Reply

The article MEMO1 (gene) has been proposed for deletion because of the following concern:

Non-notable. No evidence of in independent reliable sources secondary sources.

While all constructive contributions to Wikipedia are appreciated, content or articles may be deleted for any of several reasons.

You may prevent the proposed deletion by removing the {{proposed deletion/dated}} notice, but please explain why in your edit summary or on the article's talk page.

Please consider improving the article to address the issues raised. Removing {{proposed deletion/dated}} will stop the proposed deletion process, but other deletion processes exist. In particular, the speedy deletion process can result in deletion without discussion, and articles for deletion allows discussion to reach consensus for deletion. Stuartyeates (talk) 07:38, 29 January 2014 (UTC)Reply

This edit is clearly an error. I reverted the edit to restore the original gene. Boghog (talk) 08:02, 5 July 2014 (UTC)Reply

This recent edit is not right either. Nor this edit. It appears large numbers of the bots recent edits are in error. Boghog (talk) 08:09, 5 July 2014 (UTC)Reply

Just to let you know the bot made an error on this one and broke the image - see edit

Cheers KylieTastic (talk) 17:22, 8 August 2014 (UTC)Reply

@KylieTastic:: Thank you for catching/fixing that error! We'll be sure to fix that in the bot... Cheers, Andrew Su (talk) 17:29, 8 August 2014 (UTC)Reply

I noticed that the bot created hydroxyacid oxidase (glycolate oxidase) 1, but did not create the corresponding redirects from HAO1, HAOX1, or GOX1. I've done so now. I can understand not creating one from GOX as it was an existing DAB page, but ideally that case should be handled too. This likely is not the only such case... LeadSongDog come howl! 19:03, 26 August 2014 (UTC)Reply

Hi @LeadSongDog:, thanks for the note! At the moment we do not auto-create redirects for the gene symbol(s). Part of the answer is that we didn't want to deal with tricky issues with disambiguation (which would be common with these short acronyms). The other part is that it just hasn't reached the top of our priority list. Thanks for the feedback though -- we'll keep that in mind! (incidentally, just noticed that we previously had this idea at User:ProteinBoxBot/Ideas, but struck it with the comment "better for a human to do".) Cheers, Andrew Su (talk) 20:09, 26 August 2014 (UTC)Reply

If you're depending on humans to notice the page's creation, it might be worth adding a wikiproject template to the talkpage, so they've got a fighting chance. Also, the lede text seems to be direct copypaste, but the attribution was unclear. Am I missing something? LeadSongDog come howl! 20:24, 26 August 2014 (UTC)Reply

Yes, the bot should also create the talk page with the wikiproject templates (e.g., Talk:Melanoma_antigen_family_a,_8) -- not sure why that didn't happen for Hydroxyacid oxidase (glycolate oxidase) 1. Another potential bug we will look into. The lede is not a copypaste, but is an auto-generated template sentence that we (with WP:MCB) decided would be a good standard intro. Make sense? Cheers, Andrew Su (talk) 00:34, 27 August 2014 (UTC)Reply

Actually, at one point, systematic redirects (in the format <HUGO gene symbol> (gene)) were created for all the Gene Wiki articles (see BogBot 3 and {{R from gene symbol}}). If I am not mistaken, by default, new Gene Wiki articles that are created by the BioGPS tool are named by default<HUGO gene symbol> (gene). For completeness, HAO1 (gene), HAOX1 (gene), or GOX1 (gene) should also be created. Boghog (talk) 20:30, 26 August 2014 (UTC)Reply

The BioGPS tool to create pages gives three options for the article title, as shown here (for an already-created article). The user just selects one, and the bot does not currently create any redirects. Again, we can integrate that into the web interface and subsequent bot edit if there is consensus (and pending developer time)... Cheers, Andrew Su (talk) 00:34, 27 August 2014 (UTC)Reply

Dear all,

I am a little outdated, my last edit was years ago.

So I could not track where in the code is specified the "Available structures" but I am wondering if it is time to include, as long as you include the PDB codes, the EMDB codes.

i.e.: for RYR1, the available crystal structures correspond only to some small fragments, while in the last year, with the development of the direct detectors, a structure at 3.8 Å has been published, much more relevant:

Paper: http://www.ncbi.nlm.nih.gov/pubmed/25517095

Structure: http://www.ebi.ac.uk/pdbe/entry/EMD-2807, http://www.ebi.ac.uk/pdbe/entry/EMD-2807/visualization

I think that with the recent developments in electron microscopy, these high resolution structures are going to be more and more common, exponentially more common, and the template should be updated correspondingly.

Does anybody agree with me?

Thanks

--Flakinho (talk) 21:21, 2 March 2015 (UTC)Reply

Still might be a little too soon as the number of electron microscopy structures is still fairly limited (compare microscopy ~3,000 structures with X-ray crystallography ~100,000 structures). Boghog (talk) 22:11, 2 March 2015 (UTC)Reply

The bot is putting bogus dates in such as Retrieved 2015-03-02T13:51:00.480604-08:00. https://en.wikipedia.org/w/index.php?title=COX5A&oldid=649600502 Please don't include the entire date, minutes and all. It causes a template error. AManWithNoPlan (talk) 03:54, 3 March 2015 (UTC)Reply

Thank you, I've created a ticket for this change... Best, Andrew Su (talk) 16:53, 4 March 2015 (UTC)Reply

Hi,

Template:PBB/23405 and Template:PBB/7884 have been broken twice in two days b y the bot

Cheers KylieTastic (talk) 15:21, 10 July 2015 (UTC)Reply

Thank you for the note! We just resurrected the bot after a bit of a dormancy, and looks like there are a few bugs that have crept in. We will investigate and fix asap... Best, Andrew Su (talk) 16:09, 10 July 2015 (UTC)Reply

• Hi Andrew Su, thanks for the update - the bot did break them again so I'll leave them until you've fixed the issues. Cheers KylieTastic (talk) 09:50, 11 July 2015 (UTC)Reply

I didn't see this until after I had fixed the image. CambridgeBayWeather, Uqaqtuq (talk), Sunasuttuq 20:37, 13 July 2015 (UTC)Reply

The bot is still breaking Template:PBB/7884 over and over - and people are reverting - in fact that's most of what the bot has been doing for the last couple of days - please fix it or stop the bot until it can be fixed. breaking an image 20+ times in a row is not good. KylieTastic (talk) 20:06, 22 July 2015 (UTC)Reply

Hi, I was testing the bot and fixing it. The bot wasn't running on its own. Sorry I made the log messy. Julialturner (talk) 21:08, 22 July 2015 (UTC)Reply

Ok, no worries KylieTastic (talk) 12:47, 25 July 2015 (UTC)Reply

Hello, and welcome to Wikipedia. This is a notice to inform you that a tag has been placed on Tia1 cytotoxic granule-associated rna binding protein requesting that it be speedily deleted from Wikipedia. This has been done under section A3 of the criteria for speedy deletion, because it is an article with no content whatsoever, or whose contents consist only of external links, a "See also" section, book references, category tags, template tags, interwiki links, images, a rephrasing of the title, a question that should have been asked at the help or reference desks, or an attempt to contact the subject of the article. Please see Wikipedia:Stub for our minimum information standards for short articles. Also please note that articles must be on notable subjects and should provide references to reliable sources that verify their content.

If you think this page should not be deleted for this reason, you may contest the nomination by visiting the page and clicking the button labelled "Click here to contest this speedy deletion". This will give you the opportunity to explain why you believe the page should not be deleted. However, be aware that once a page is tagged for speedy deletion, it may be removed without delay. Please do not remove the speedy deletion tag from the page yourself, but do not hesitate to add information in line with Wikipedia's policies and guidelines. If the page is deleted, and you wish to retrieve the deleted material for future reference or improvement, then please contact the deleting administrator, or if you have already done so, you can place a request here. Malcolmxl5 (talk) 19:54, 13 July 2015 (UTC)Reply

Would it be possible for the bot to make captions using the {{PDB}} template to more easily link out to the relevant structure in the PDB? E.g "Rendering based on PDB: 1l9x​" T.Shafee(Evo﹠Evo)^talk 12:46, 15 July 2015 (UTC)Reply

Thank you for the suggestion. We currently have a link below the image under "List of PDB id codes", but I will look into adding it to the caption in addition. Cheers, Julia Turner (talk) 20:38, 16 July 2015 (UTC)Reply

Hello, why you did this: https://en.wikipedia.org/w/index.php?title=Template:PBB/1234&diff=670617304&oldid=669248415 on PBB/1234 used in CCR5?

Revision as of 02:48, 9 July 2015 (edit) (undo)
ProteinBoxBot (talk | contribs)
m (Updated 5 fields: Component, Hs_GenLoc_db, Hs_GenLoc_start, PDB, Hs_GenLoc_end)

- | image = CCR5+membrane1.png | image_source = PDB rendering based on 4mbs (yellow) in cell membrane (grey).

+ | image = Protein_CD44_PDB_1poz.png
+ | image_source = PDB rendering based on 1poz.

CD44 is not CCR5; 1poz is not CCR5. Pleasy undo your changes. (check Talk:CCR5#Picture of wrong protein in info box) `a5b (talk) 13:55, 20 July 2015 (UTC)Reply

Thank you for pointing out this image error. This is a bug that should be corrected and the image should not be overwritten by the bot. Julia Turner (talk) 14:55, 20 July 2015 (UTC)Reply

They will be removed.Xx236 (talk) 09:58, 17 August 2015 (UTC) Is a redirect interesting for two projects HINT2 (gene)?~~Reply

Obviously the article is no longer a blank, it has been converted into a redirect with the {{R from gene symbol}} template added. Furthermore a systematic effort has been made to create redirects from "<Gene symbol> (gene)" → "<Gene symbol>" making it easier to find these articles. The HINT2 article was apparently created without the help of the bot. There was missing material in HINT2 so I triggered the bot to create the HINT2 (gene) article in an attempt to get the bot to generate the missing material which I then intended to merge back into the original article leaving behind a redirect. Since no material was added, I just converted the blank article into the redirect. No permanent harm done. Boghog (talk) 11:04, 17 August 2015 (UTC)Reply

For more information follow the category link. - which category link?Xx236 (talk) 11:10, 17 August 2015 (UTC)Reply

Huntingtin interacting protein 1 is still blank.Xx236 (talk) 11:11, 17 August 2015 (UTC)Reply

Category:Redirects from gene symbols. {{sofixit}} Boghog (talk) 12:08, 17 August 2015 (UTC)Reply

Hello, and welcome to Wikipedia. This is a notice to inform you that a tag has been placed on Aconitase 2, mitochondrial requesting that it be speedily deleted from Wikipedia. This has been done under section A3 of the criteria for speedy deletion, because it is an article with no content whatsoever, or whose contents consist only of external links, a "See also" section, book references, category tags, template tags, interwiki links, images, a rephrasing of the title, a question that should have been asked at the help or reference desks, or an attempt to contact the subject of the article. Please see Wikipedia:Stub for our minimum information standards for short articles. Also please note that articles must be on notable subjects and should provide references to reliable sources that verify their content.

If you think this page should not be deleted for this reason, you may contest the nomination by visiting the page and clicking the button labelled "Contest this speedy deletion". This will give you the opportunity to explain why you believe the page should not be deleted. However, be aware that once a page is tagged for speedy deletion, it may be removed without delay. Please do not remove the speedy deletion tag from the page yourself, but do not hesitate to add information in line with Wikipedia's policies and guidelines. If the page is deleted, and you wish to retrieve the deleted material for future reference or improvement, then please contact the deleting administrator, or if you have already done so, you can place a request here. —Godsy^(TALK_CONT) 04:28, 5 September 2015 (UTC)Reply

Hello ProteinBoxBot,

I wanted to let you know that I just tagged IFITM5 for deletion, because it doesn't appear to contain any encyclopedic content. Take a look at our suggestions for essential content in short articles to learn what should be included.

If you feel that the article shouldn't be deleted and want more time to work on it, you can contest this deletion, but please don't remove the speedy deletion tag from the top.

You can leave a note on my talk page if you have questions. Trivialist (talk) 16:16, 5 September 2015 (UTC)Reply

Hello, and welcome to Wikipedia. This is a notice to inform you that a tag has been placed on DPEP2 (gene) requesting that it be speedily deleted from Wikipedia. This has been done under section A3 of the criteria for speedy deletion, because it is an article with no content whatsoever, or whose contents consist only of external links, a "See also" section, book references, category tags, template tags, interwiki links, images, a rephrasing of the title, a question that should have been asked at the help or reference desks, or an attempt to contact the subject of the article. Please see Wikipedia:Stub for our minimum information standards for short articles. Also please note that articles must be on notable subjects and should provide references to reliable sources that verify their content.

If you think this page should not be deleted for this reason, you may contest the nomination by visiting the page and clicking the button labelled "Contest this speedy deletion". This will give you the opportunity to explain why you believe the page should not be deleted. However, be aware that once a page is tagged for speedy deletion, it may be removed without delay. Please do not remove the speedy deletion tag from the page yourself, but do not hesitate to add information in line with Wikipedia's policies and guidelines. If the page is deleted, and you wish to retrieve the deleted material for future reference or improvement, then please contact the deleting administrator, or if you have already done so, you can place a request here. Gronk Oz (talk) 03:19, 1 November 2015 (UTC)Reply

Thanks for uploading File:PBB Protein TTN image.jpg. I noticed that while you provided a valid copyright licensing tag, there is no proof that the creator of the file has agreed to release it under the given license.

If you are the copyright holder for this media entirely yourself but have previously published it elsewhere (especially online), please either

• make a note permitting reuse under the CC-BY-SA or another acceptable free license (see this list) at the site of the original publication; or
• Send an email from an address associated with the original publication to [email protected], stating your ownership of the material and your intention to publish it under a free license. You can find a sample permission letter here. If you take this step, add {{OTRS pending}} to the file description page to prevent premature deletion.

If you did not create it entirely yourself, please ask the person who created the file to take one of the two steps listed above, or if the owner of the file has already given their permission to you via email, please forward that email to [email protected].

If you believe the media meets the criteria at Wikipedia:Non-free content, use a tag such as {{non-free fair use}} or one of the other tags listed at Wikipedia:File copyright tags#Fair use, and add a rationale justifying the file's use on the article or articles where it is included. See Wikipedia:File copyright tags for the full list of copyright tags that you can use.

If you have uploaded other files, consider checking that you have provided evidence that their copyright owners have agreed to license their works under the tags you supplied, too. You can find a list of files you have created in your upload log. Files lacking evidence of permission may be deleted one week after they have been tagged, as described on criteria for speedy deletion. You may wish to read Wikipedia's image use policy. If you have any questions please ask them at the Media copyright questions page. Thank you. Stefan2 (talk) 21:40, 3 November 2015 (UTC)Reply

Hello, and welcome to Wikipedia. This is a notice to inform you that a tag has been placed on Ndufa4, mitochondrial complex associated requesting that it be speedily deleted from Wikipedia. This has been done under section A3 of the criteria for speedy deletion, because it is an article with no content whatsoever, or whose contents consist only of external links, a "See also" section, book references, category tags, template tags, interwiki links, images, a rephrasing of the title, a question that should have been asked at the help or reference desks, or an attempt to contact the subject of the article. Please see Wikipedia:Stub for our minimum information standards for short articles. Also please note that articles must be on notable subjects and should provide references to reliable sources that verify their content.

If you think this page should not be deleted for this reason, you may contest the nomination by visiting the page and clicking the button labelled "Contest this speedy deletion". This will give you the opportunity to explain why you believe the page should not be deleted. However, be aware that once a page is tagged for speedy deletion, it may be removed without delay. Please do not remove the speedy deletion tag from the page yourself, but do not hesitate to add information in line with Wikipedia's policies and guidelines. If the page is deleted, and you wish to retrieve the deleted material for future reference or improvement, then please contact the deleting administrator, or if you have already done so, you can place a request here. — Smjg (talk) 18:40, 1 December 2015 (UTC)Reply

Hello, and welcome to Wikipedia. This is a notice to inform you that a tag has been placed on Patched 2 requesting that it be speedily deleted from Wikipedia. This has been done under section A3 of the criteria for speedy deletion, because it is an article with no content whatsoever, or whose contents consist only of external links, a "See also" section, book references, category tags, template tags, interwiki links, images, a rephrasing of the title, a question that should have been asked at the help or reference desks, or an attempt to contact the subject of the article. Please see Wikipedia:Stub for our minimum information standards for short articles. Also please note that articles must be on notable subjects and should provide references to reliable sources that verify their content.

If you think this page should not be deleted for this reason, you may contest the nomination by visiting the page and clicking the button labelled "Contest this speedy deletion". This will give you the opportunity to explain why you believe the page should not be deleted. However, be aware that once a page is tagged for speedy deletion, it may be removed without delay. Please do not remove the speedy deletion tag from the page yourself, but do not hesitate to add information in line with Wikipedia's policies and guidelines. If the page is deleted, and you wish to retrieve the deleted material for future reference or improvement, then please contact the deleting administrator, or if you have already done so, you can place a request here. Xx236 (talk) 11:07, 21 December 2015 (UTC)Reply

Hi, your bot used an incorrect template when marking an article as a stub. It used {{Gene--stub}} instead of the proper {{gene-stub}} . In veritas (talk) 05:28, 18 February 2016 (UTC)Reply

Thank you for helping us identify bugs. Can you provide an example? I checked a few recent articles and they seem correct. Thanks Julialturner (talk) 06:46, 19 February 2016 (UTC)Reply

Sure, here is one: [example 1] and [2] In veritas (talk) 18:34, 21 February 2016 (UTC)Reply

This bug should be no longer occur. Thank you for you providing examples. Julialturner (talk) 07:21, 22 February 2016 (UTC) @In veritas:Reply

The article NFE2L1 has been proposed for deletion because of the following concern:

The entire article seems to be derived from original research materials, especially toward research gate. Wikipedia is not a publisher of research. WP:OR

While all constructive contributions to Wikipedia are appreciated, content or articles may be deleted for any of several reasons.

You may prevent the proposed deletion by removing the {{proposed deletion/dated}} notice, but please explain why in your edit summary or on the article's talk page.

Please consider improving the article to address the issues raised. Removing {{proposed deletion/dated}} will stop the proposed deletion process, but other deletion processes exist. In particular, the speedy deletion process can result in deletion without discussion, and articles for deletion allows discussion to reach consensus for deletion. Winterysteppe (talk) 21:52, 26 February 2016 (UTC)Reply

Template:PBB/2155 has been nominated for deletion. You are invited to comment on the discussion at the template's entry on the Templates for discussion page. Ricky81682 (talk) 23:44, 2 March 2016 (UTC)Reply

Hi, it should be easy to correct some things that your bot is doing incorrectly:

• "Further Reading": wrong capitalization (should be "Further reading"); also, I don't think this section should be added if it is empty like in this case.
• Under "Function", there's a reference, even including the PMID. This should make it exceedingly easy to include a completely formatted reference enclosed by ref tags, so that it actually appears in the references section....
• Perhaps the text under "function" could be modified to actually be a sentence.

Hope this helps. --Randykitty (talk) 12:59, 9 March 2016 (UTC)Reply

@Randykitty Thank you for your suggestions. I am currently working on updating the code for the Further reading section and it shouldn't display empty results in the near future. The function text does look strange for this particular gene and I will look into why and how I can create better sentence structure and ref tags. Julialturner (talk) 05:38, 10 March 2016 (UTC)Reply

Thanks for uploading File:PBB Protein SNCA image.jpg, which you've attributed to www.pdb.org. I noticed that while you provided a valid copyright licensing tag, there is no proof that the creator of the file has agreed to release it under the given license.

If you are the copyright holder for this media entirely yourself but have previously published it elsewhere (especially online), please either

• make a note permitting reuse under the CC-BY-SA or another acceptable free license (see this list) at the site of the original publication; or
• Send an email from an address associated with the original publication to [email protected], stating your ownership of the material and your intention to publish it under a free license. You can find a sample permission letter here. If you take this step, add {{OTRS pending}} to the file description page to prevent premature deletion.

If you did not create it entirely yourself, please ask the person who created the file to take one of the two steps listed above, or if the owner of the file has already given their permission to you via email, please forward that email to [email protected].

If you believe the media meets the criteria at Wikipedia:Non-free content, use a tag such as {{non-free fair use}} or one of the other tags listed at Wikipedia:File copyright tags#Fair use, and add a rationale justifying the file's use on the article or articles where it is included. See Wikipedia:File copyright tags for the full list of copyright tags that you can use.

If you have uploaded other files, consider checking that you have provided evidence that their copyright owners have agreed to license their works under the tags you supplied, too. You can find a list of files you have created in your upload log. Files lacking evidence of permission may be deleted one week after they have been tagged, as described on criteria for speedy deletion. You may wish to read Wikipedia's image use policy. If you have any questions please ask them at the Media copyright questions page. Thank you. Stefan2 (talk) 19:49, 12 May 2016 (UTC)Reply

Thanks for uploading File:PBB Protein GTPBP9 image.jpg, which you've attributed to www.pdb.org. I noticed that while you provided a valid copyright licensing tag, there is no proof that the creator of the file has agreed to release it under the given license.

If you are the copyright holder for this media entirely yourself but have previously published it elsewhere (especially online), please either

• make a note permitting reuse under the CC-BY-SA or another acceptable free license (see this list) at the site of the original publication; or
• Send an email from an address associated with the original publication to [email protected], stating your ownership of the material and your intention to publish it under a free license. You can find a sample permission letter here. If you take this step, add {{OTRS pending}} to the file description page to prevent premature deletion.

If you did not create it entirely yourself, please ask the person who created the file to take one of the two steps listed above, or if the owner of the file has already given their permission to you via email, please forward that email to [email protected].

If you believe the media meets the criteria at Wikipedia:Non-free content, use a tag such as {{non-free fair use}} or one of the other tags listed at Wikipedia:File copyright tags#Fair use, and add a rationale justifying the file's use on the article or articles where it is included. See Wikipedia:File copyright tags for the full list of copyright tags that you can use.

If you have uploaded other files, consider checking that you have provided evidence that their copyright owners have agreed to license their works under the tags you supplied, too. You can find a list of files you have created in your upload log. Files lacking evidence of permission may be deleted one week after they have been tagged, as described on criteria for speedy deletion. You may wish to read Wikipedia's image use policy. If you have any questions please ask them at the Media copyright questions page. Thank you. Stefan2 (talk) 20:19, 12 May 2016 (UTC)Reply

Hi, I've been working on Category:CS1 maint: Multiple names: authors list and I've noticed that the vast majority of {{PBB Further reading}} transclusions simply require |author= be changed to |vauthors= to avoid being placed into this maintenance category (examples [1], [2], [3]). Please update the bot to minimize future maintenance. Thank you!   ~ Tom.Reding (talk ⋅dgaf)  16:53, 22 May 2016 (UTC)Reply

@Tom.Reding:. Hi Tom, I did a quick check of the article generation tool and it is no longer using the |author= as described above, but instead the vauthors syntax. Thanks Julialturner (talk) 21:45, 22 May 2016 (UTC)Reply

Great! Thanks for checking.   ~ Tom.Reding (talk ⋅dgaf)  21:53, 22 May 2016 (UTC)Reply

Hi, I've been replacing 'missing' categories for quite a few well-sourced proteins/enzymes for awhile now but on deeper investigation I think this bot is somehow causing the existing categories to be dropped. Have a look at this edit in relation to the previous version: https://en.wikipedia.org/w/index.php?title=CHD2&direction=next&oldid=696051398 It showed Category:Human proteins before the edit but then somehow got dropped.--Hooperbloob (talk) 06:21, 25 May 2016 (UTC)Reply

• Ditto for this one: https://en.wikipedia.org/w/index.php?title=AP4S1&direction=next&oldid=720402628 --Hooperbloob (talk) 06:23, 25 May 2016 (UTC)Reply

Thanks Hooperbloob, this is really weird. Some of the articles with the new gene infobox are still in that category but it does seem like many are no longer - as in the examples you point out. Investigating.. --Benjamin Good (talk) 15:20, 25 May 2016 (UTC)Reply

Ok, good to know I wasn't just seeing things. Unfortunately I'm not a biology expert so many of the categories I 'restored' are likely much simpler than the ones that were there originally. Maybe a script could go through this bots edits and do before/after comparisons.Hooperbloob (talk) 16:03, 25 May 2016 (UTC)Reply

Any progress in figuring out the issue? It looks like infoboxes are contributing categories to articles by their mere inclusion. Have a look at this one: https://en.wikipedia.org/wiki/WHSC2 No cats shown in the source but yet they still appear in the published content. Bots that patrol for uncategorized articles can't divine their presence so they step in and tag them as uncategorized.Hooperbloob (talk) 21:30, 13 June 2016 (UTC)Reply

Hi Hooperbloob. We found that the migration to the new infobox did indeed result in the loss of those categories. To fix that, we adapted the Lua code that produces the infobox such that the categories are all now rendered on the page. This actually resulted in a significantly higher accuracy of categorization than before. In particular, all of the chromosome categories are now correct and complete with respect to what genes exist in Wikipedia. This looks to me like an error in the implementation of the bot patrolling for uncategorized articles. The categories are there and are usable. --Benjamin Good (talk) 21:43, 13 June 2016 (UTC)Reply

FWIW, AWB's "auto tag" feature removes {{uncat}} from WHSC2 when no explicit categories are present. I can't speak to other automated editing software though.   ~ Tom.Reding (talk ⋅dgaf)  21:50, 13 June 2016 (UTC)Reply

Where is the bot that adds the uncategorized tag ? If it checked the API, e.g. https://en.wikipedia.org/w/api.php?action=query&titles=WHSC2&prop=categories it could see the categories here. --Benjamin Good (talk) 21:59, 13 June 2016 (UTC)Reply

I think the categorization derivation via infoboxes is a neat trick, definitely more accurate. However, the problems seem multifold:

• its not obvious to editors who don't know how it works,

I added a note about this to the infobox gene documentation as a start.

• articles missing explicit cats get tagged as uncategorized by people or bots,

This really seems like something that needs to be fixed by the bot authors. I don't see why people would add the tag when they can consistently see the generated categories on the article?

• not sure what happens if explicit cats are added, they seem to mask the derived ones.

I tested this and did not see that behavior. Adding additional categories seems to work as you would expect. If not, could you link an example?

Maybe the ProteinBoxBot could include a hidden link/comment at the bottom of the article telling editors whats going on.

Okay we will look into that. Thanks for the suggestion. --Benjamin Good (talk) 16:41, 15 June 2016 (UTC)Reply

I'm sure what bot is tagging the "uncategorized" articles.Hooperbloob (talk) 16:23, 15 June 2016 (UTC)Reply

Please do not add an underscore between the words Infobox and gene. It makes code readability more difficult. -- Magioladitis (talk) 08:15, 6 June 2016 (UTC)Reply

Hi, @Magioladitis: actually I find the use of the underscore more intuitive because it maps precisely and this might make it more easily interpreted by new wiki users. However, if a user changes the underscore to a space I could do a check so the bot doesn't overwrite it. Julialturner (talk) 21:40, 6 June 2016 (UTC)Reply

I'd like to improve some of the gene stubs, editing the article text and see also, not the references, infobox, or further reading. However it seems that PBB will overwrite whatever I do - or will it? The five-year-old discussion here says that it actually doesn't. Another editor wondered about it.

Does PBB overwrite summaries? If not, perhaps the templates and their documentation could be updated. If so, what's the best way to improve the pages without having the changes overwritten? Set require manual inspection to yes, set update summary to no, or something else entirely?

Thanks. BlackcurrantTea (talk) 06:16, 4 February 2017 (UTC)Reply

Hi BlackcurrantTea, our bot will not overwrite any edits you make. Currently, our bot only maintains values in the right-hand infobox, and all that data is being drawn from wikidata. Edit away please! And if in the course of editing you would like to remove some of our old template (example diff) please do! Your message is a good reminder that we should write a bot to do that en masse... Best, Andrew Su (talk) 06:24, 4 February 2017 (UTC)Reply

Thanks, will do! BlackcurrantTea (talk) 06:42, 4 February 2017 (UTC)Reply

Hi, I'm Robert McClenon. I wanted to let you know that I saw the page you reviewed, Long intergenic non-protein coding rna 312, and have un-reviewed it again. If you have any questions, please ask them on my talk page. Thank you.

Robert McClenon (talk) 01:23, 23 March 2017 (UTC)Reply

Just to let you know that the template Template:PBB/54586 used at EQTN is a redlink. Please ignore me if it's supposed to be like that! Shhhnotsoloud (talk) 14:39, 25 May 2017 (UTC)Reply

fixed ! --Benjamin Good (talk) 15:20, 25 May 2017 (UTC)Reply

Hi, the template {{PBB|geneid=343472}} on page BARHL2 is a redlink, is this something you can fix? Thanks. DferDaisy (talk) 00:07, 20 July 2017 (UTC)Reply

Thanks for the message! For posterity's sake, Gstupp addressed this particular issue in this edit. I've also created a github issue to add fixing all other examples like this to our to-do list. Best, Andrew Su (talk) 19:07, 31 July 2017 (UTC)Reply

... and thanks to Julialturner, all transclusions of {{PBB}} in the main namespace have now been removed. Best, Andrew Su (talk) 15:54, 1 August 2017 (UTC)Reply

Sorry If I disturb You, I'm a French woman who knows a 9 years old girl named Elena that have this micro deletion. Her mother created an association in france to help her (Un pas vers l'autonomie) Did you find in the different sources you have read about it, something talking about therapies for children suffering of this illness. Or about associations of people having this PPP2r5c ? Please let me a message on my profile if you have some informations. https://fr.wikipedia.org/wiki/Utilisateur:Felina — Preceding unsigned comment added by Felina (talk • contribs) 22:17, 4 December 2017 (UTC)Reply

Hello ProteinBoxBot,

I wanted to let you know that I just tagged EYCL1 (gene) for deletion, because it appears to duplicate an existing Wikipedia article, Eye color 1 (green/blue).

If you feel that the article shouldn't be deleted, you can contest this deletion, but please don't remove the speedy deletion tag from the top.

You can leave a note on my talk page if you have questions.

Slatersteven (talk) 17:09, 9 March 2018 (UTC)Reply

In Stt3a, catalytic subunit of the oligosaccharyltransferase complex §Further reading, Ghosh et al. shows a Vancouver style error. Bots should not be creating errors that human editors must repair. Please fix the bot.

—Trappist the monk (talk) 13:37, 12 July 2018 (UTC)Reply

And still the bot is creating errors for humans to cleanup: Elongation factor for rna polymerase ii 2 §Further reading. Please fix this.

Also, why is §Further reading not alpha sorted by primary author surname?

—Trappist the monk (talk) 15:01, 24 August 2018 (UTC)Reply

At the time the bot was created, I believe references were compliant with the standards (and community consensus) at the time. We will look at amending the bot with this newer guidance, but that will take some time. The other option is to shut the bot off in the mean time, but I think that would be throwing the baby out with the bath water... Best, Andrew Su (talk) 19:59, 24 August 2018 (UTC)Reply

@Andrew Su: This is a trivial fix that can be quickly implemented. According to the "NLM Author Indexing Policy":

• Convert given (first) names and middle names to initials for a maximum of two initials.^[1]

It appears that National Library of Medicine (NLM) has "extended" the standard from two to three characters, but I cannot find any statement from the NLM about this deviation. The |vauthors = parameter of WP:Citation Style 1 follows the published guidance. Boghog (talk) 21:31, 24 August 2018 (UTC)Reply

Hi. I see that you uploaded a bunch of images from www.pdb.org, e.g. File:PBB Protein EIF3S9 image.jpg. Can you please provide a link somewhere to evidence that these images are public domain? Thanks. --B (talk) 21:36, 22 August 2018 (UTC)Reply

Hello, these were generated by PDBe. Way back when, we confirmed that those were public domain, but truthfully I'm forgetting the details. Either it was personal communication with the person who generated the images, or it was a page on the website that has now been removed. I wish I had more details (and added it to the metadata) but alas... Best, Andrew Su (talk) 19:56, 24 August 2018 (UTC)Reply

Hi, in the "Further reading" sections that are created by the bot there is {{refbegin | 2}} inserted. This does not give a good result for widescreen monitors or narrow screen phones, so to remedy that, variable columnisation should be used, say with this: {{refbegin | 30em}}. Graeme Bartlett (talk) 01:52, 25 August 2018 (UTC)Reply

Like that one. Probably they should not be created by this bot? My very best wishes (talk) 16:54, 30 August 2018 (UTC)Reply

Even though it is non-coding, it is still a gene and therefore arguably within the scope of {{Infobox gene}}. There used to be a |NotAProtein=yes parameter to in the previous {{GNF Protein box}} to suppress the automatic addiction of category:Human proteins (see discussion). The infobox no longer adds these categories, so the parameter is no longer needed. Boghog (talk) 17:52, 30 August 2018 (UTC)Reply

Yes, I also see H19 (gene), for example. OK. My very best wishes (talk) 18:38, 30 August 2018 (UTC)Reply

But one must make a different bot for creating pages about non-coding RNA... The boxes on all such pages are meaningless. However, I did not mark any of them for deletion if the bot created meaningful text. My very best wishes (talk) 02:38, 6 October 2018 (UTC)Reply

I have temporarily blocked this bot because it seemed to be malfunctioning. Feel free to unblock (without consultation) when the problem is fixed.

It created today TSPYL5 (gene) (seems to be the correct page), TSPYL5 (duplicate) and Tspy like 5 (duplicate). Both duplicates also have the error "An Error has occurred retrieving Wikidata item for infobox" in plain text at the top of the article, and no infobox. The bot should probably not create articles for aliases, but simply redirects instead? And some check to avoid the Wikidata error would be good as well (I'll not suggest my prefered solution to this, as that is not really relevant for the bot block). Fram (talk) 06:57, 6 September 2018 (UTC)Reply

@Andrew Su: It look like this might be caused by duplicate protein records in wikidata? Q21123506 and Q21987041

@Fram: thanks for your note. After looking at this more, I'm still not exactly sure what happened. Our bot creates articles on demand through http://biogps.org/genewikigenerator (e.g., TSPYL5), which is linked from Editing FAQ #5 at WP:Gene_Wiki. That interface provides suggested WP page names, but allows users to override those suggestions. The interface is also designed to detect when a WP page for a gene already exists so that duplicates are not created. That generally works fine, but looks like this user somehow managed to use our "name override" feature while bypassing the "duplicate check". Again, not quite sure how s/he did that. However, given that this is the first time we've seen this issue for a system that has been running unattended for a couple years, I suggest that we unblock and continue to keep an eye on this. The duplicates can also be flagged for deletion. Does this plan seem reasonable to you? (@71.218.74.130: the two WD items you linked are for the human and mouse genes, respectively. So no, that is not the root of this issue here...) Best, Andrew Su (talk) 21:23, 6 September 2018 (UTC)Reply

and on second thought, I changed the two duplicate pages at TSPYL5 and Tspy like 5 to redirect to TSPYL5 (gene). Best, Andrew Su (talk) 21:27, 6 September 2018 (UTC)Reply

@Andrew Su: Why the box does not work for T cell receptor beta constant 1? There are no links to Uniprot, etc. It is this protein. My very best wishes (talk) 05:08, 15 September 2018 (UTC)Reply

@My very best wishes: Sorry for the slow reply. Most of that infobox is not filled because the corresponding information is not available in the corresponding wikidata item. Our Wikidata bot in turn draws primarily from the gene page on NCBI, and you can see that information (refseq protein, Ensembl cross references, etc.) is not there either. So this appears to be a data issue with the source databases, and not a bot/infobox/wikidata issue... Best, Andrew Su (talk) 04:39, 26 September 2018 (UTC)Reply

How come? I followed your NCBI link (liked from Wikidata) and it does provide links to Refseq, UniProt, etc. So, this appear to be an error by the bot, or maybe the Refseq link did not exist at the time when this WP page was created? If so, one should re-run bot? But if I understand correctly, the bot regularly updates these pages anyway? So, this should be something wrong with the bot. I suspect there are many such pages. In any event, the infobox in the page is wrong and it needs to be fixed manually or by the bot. My very best wishes (talk) 14:28, 27 September 2018 (UTC)Reply

@My very best wishes: Hmm, after looking at this more, this is a bit of an edge case it seems. In the case of T cell receptor beta constant 1, there are two things you point out. First, Wikidata does not have refseq identifiers because we specifically only take transcript and protein identifiers -- in this case, only genomic Refseq are provided by NCBI. Second (and more oddly), there is the issue of the missing Uniprot. The bot runs based on mygene.info which preferentially uses NCBI Gene as its primary identifier. Uniprot mappings usually come from Ensembl, and the mappings between NCBI Gene And Ensembl depend on the cross references that both NCBI and Ensembl provide. Unfortunately neither NCBI nor Ensembl provide the mapping between the NCBI gene for TRBC1 and the Ensembl gene for TRBC1 (probably in part due to the fact that Ensembl has two gene identifiers here -- ENSG00000281981 and ENSG00000211751). All *three* of those gene entries map to the same HGNC entry (though HGNC does not map back to ENSG00000281981). So this is clearly a muddled situation in terms of the source databases. Clearly the analysis above points out additional heuristics that could be used in the bot, but we'd need to test that extensively to be sure we weren't exposing yet other problems. In the mean time, you are welcome to fix those entries by hand in wikidata. Best, Andrew Su (talk) 03:26, 3 October 2018 (UTC)Reply

Well, this is your bot. Hence it is your responsibility to fix whatever it does wrong. In this example, this is a well studied protein, but your bot created a ridiculous page that can only be deleted. My very best wishes (talk) 04:43, 4 October 2018 (UTC)Reply

OK, I will "Prod" every page that failed to provide any meaningful information except link to Entrez. My very best wishes (talk) 01:51, 6 October 2018 (UTC)Reply

So, I just prodded 12 recent pages. Other recent pages created by the bot can stay, in my opinion. My very best wishes (talk) 02:28, 6 October 2018 (UTC)Reply

Feel free to unblock if the problems are not directly with the bot, but more with the list of articles to create. If you can find a solution to avoid the Wikidata errors, that would be great, but not really essential for the running of this bot I guess. Fram (talk) 06:08, 7 September 2018 (UTC)Reply

This user's unblock request has been reviewed by an administrator, who accepted the request.

ProteinBoxBot (block log • active blocks • global blocks • contribs • deleted contribs • filter log • creation log • change block settings • unblock • checkuser (log) • SI)

---

Request reason:

Requesting unblock per discussion above with User:Fram, who originally initiated the block. TLDR: this duplicate entry creation appears to be an extremely rare case, and one that we bot owners will keep a close eye on.

Accept reason:

As per above. Boing! said Zebedee (talk) 18:29, 7 September 2018 (UTC)Reply

• Shoud we produce any pages about pseudogenes, such as that one? Seriously, one needs at least one reference to a publication in a scientific journal. The record ("publication") in Entrez is not just a primary source, but a poor quality primary source. My very best wishes (talk) 20:54, 21 October 2018 (UTC)Reply

I made it a redirect. My very best wishes (talk) 14:54, 22 October 2018 (UTC)Reply

I would agree that most pseudogenes are not notable. However one should not make a blanket assumption that all lack notablilty (see for example: this and this). Entrez is tertiary source (a database), and within the scope of databases, IMHO, a high quality source. Finally I agree that Sec24 homolog a pseudogene 1, as it lack homologs is not notable and a redirect is appropriate. Boghog (talk) 19:47, 22 October 2018 (UTC)Reply

Thank you! Yes, I see Entrez gives this as a "primary source". I still think we need at least one publication in a scientific journal to tell that something was notable enough for inclusion. Saying that, I agree with creating any pages that provide correct linking to other multiple resources (such as Uniprot) or some meaningful information. I also agree that certain pseudogenes would qualify for inclusion. My very best wishes (talk) 23:20, 22 October 2018 (UTC)Reply

But, looking at something like that, this is based exclusively on that database ref. Of course, one could create a page, Multiple sclerosis susceptibility loci and there are sources [4] (and it would not even mention "MS4"), however, as created by the bot, this is just a spam. My very best wishes (talk) 19:02, 23 October 2018 (UTC)Reply

Here is litmus test: link to PubMed from the protein box [5]. My very best wishes (talk) 19:14, 23 October 2018 (UTC)Reply

Can some editors who know this branch of science better please go through the bot creations and move the pages to the correct capitalization? Many pages are created with an incorrect capitalization, and as a non-specialist it is rather time-consuming to find the right capitalization in each case. I moved MLLT6, PHD finger containing but pages like Sft2 domain containing 2, Family with sequence similarity 111 member a, Tetratricopeptide repeat domain 21b, Tnrc6c antisense rna 1, Late endosomal/lysosomal adaptor, mapk and mtor activator 1, Ret finger protein like 4a, Ras p21 protein activator 2, ... all seem to need to be page moved. Fram (talk) 07:43, 23 October 2018 (UTC)Reply

I have blocked the bot again, as the creations have too many problems. There are the capitalization errors (see my post above, see also the latest creation Microrna 93; there are pages that get redirected after creation as they are nearly empty (Multiple sclerosis, susceptibility to, 2). And there are creations which are typos (Multiple sclerosis, susceptiblity to, 4). These are the three most recent creations, and we get three different problems, which is a bit too much to allow bot creations to continue (see also pages with errors, which already led to the previous block, but continued afterwards: e.g. Lung cancer 1). Fram (talk) 08:09, 24 October 2018 (UTC)Reply

I think most pages created by the bot are fine. Some others should be fixed manually. I can do it if the bot will be unblocked. My very best wishes (talk) 21:16, 18 November 2018 (UTC)Reply

Just a heads up that the group of templates used by the bot have been nominated for deletion, please see Wikipedia:Templates for discussion/Log/2019 March 9#Template:PBB Controls. – Uanfala (talk) 19:08, 9 March 2019 (UTC)Reply

Template:PDB Gallery has been nominated for deletion. You are invited to comment on the discussion at the template's entry on the Templates for discussion page. {{3x|p}}ery (talk) 14:55, 10 March 2019 (UTC)Reply

The file File:PBB GE NIPA1 gnf1h07157 at tn.png has been proposed for deletion because of the following concern:

unused, low-res, no obvious use

While all constructive contributions to Wikipedia are appreciated, pages may be deleted for any of several reasons.

You may prevent the proposed deletion by removing the {{proposed deletion/dated files}} notice, but please explain why in your edit summary or on the file's talk page.

Please consider addressing the issues raised. Removing {{proposed deletion/dated files}} will stop the proposed deletion process, but other deletion processes exist. In particular, the speedy deletion process can result in deletion without discussion, and files for discussion allows discussion to reach consensus for deletion.

This bot DID NOT nominate any file(s) for deletion; please refer to the page history of each individual file for details. Thanks, FastilyBot (talk) 01:01, 2 December 2019 (UTC)Reply

Hi, I have been unable to make a page for the human gene RPL22L1 via the standard process using Gene Wiki, even though the gene information is available on BioGPS. Though a paralog of the ribosomal protein RPL22, this gene is unique (~70% identical) and I think deserving of its own page for this and a few additional reasons. Could someone help me make this page (maybe @Andrew Su:) and perhaps explain why this is not working so I can fix it on my own in the future? Thanks, --PiWi

The bot has been blocked from making edits to Wikipedia, but the BioGPS tool can still create wiki text that can manually be copy and pasted into Wikipedia article (see for example RPL22L1 and hit the "Toggle Stub Code" instead of the "Create" button). You will also need to add the newly created page name to the corresponding Wikidata item (e.g., d:Q18053193, edit Wikipedia data item near the bottom of the page). Boghog (talk) 09:25, 3 December 2019 (UTC)Reply

Many thanks @Boghog: it worked perfectly!

Hello, and welcome to Wikipedia. This is a notice to inform you that a tag has been placed on Immunoglobulin superfamily member 3 requesting that it be speedily deleted from Wikipedia. This has been done under section A3 of the criteria for speedy deletion, because it is an article with no content whatsoever, or whose contents consist only of external links, a "See also" section, book references, category tags, template tags, interwiki links, images, a rephrasing of the title, a question that should have been asked at the help or reference desks, or an attempt to contact the subject of the article. Please see Wikipedia:Stub for our minimum information standards for short articles. Also please note that articles must be on notable subjects and should provide references to reliable sources that verify their content.

If you think this page should not be deleted for this reason, you may contest the nomination by visiting the page and clicking the button labelled "Contest this speedy deletion". This will give you the opportunity to explain why you believe the page should not be deleted. However, be aware that once a page is tagged for speedy deletion, it may be deleted without delay. Please do not remove the speedy deletion tag from the page yourself, but do not hesitate to add information in line with Wikipedia's policies and guidelines. If the page is deleted, and you wish to retrieve the deleted material for future reference or improvement, then please contact the deleting administrator, or if you have already done so, you can place a request here. Industrial Arthropod (talk) 17:47, 16 November 2022 (UTC)Reply

The article COPD26 has been proposed for deletion because of the following concern:

The article is based on on a record in single database (created by a bot), and the record is now discontinued.

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The article Breast cancer–related regulator of tp53 has been proposed for deletion because of the following concern:

No indication of importance.

While all constructive contributions to Wikipedia are appreciated, pages may be deleted for any of several reasons.

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Please consider improving the page to address the issues raised. Removing {{proposed deletion/dated}} will stop the proposed deletion process, but other deletion processes exist. In particular, the speedy deletion process can result in deletion without discussion, and articles for deletion allows discussion to reach consensus for deletion. Folkezoft (talk) 18:36, 30 August 2024 (UTC)Reply

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A discussion is taking place as to whether the article Suppression of tumorigenicity 8 (ovarian) is suitable for inclusion in Wikipedia according to Wikipedia's policies and guidelines or whether it should be deleted.

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

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Hello, and thank you for your contributions to Wikipedia. An article you created or substantially edited may not conform to Wikipedia's content policies and has therefore been blanked and redirected. Common reasons include that the article's subject appears to fail our notability guidelines; that the article is unsourced or poorly sourced, or that there is already an article on the same topic. The previous content is preserved in the page history. If you believe this action was taken in error, or if you have questions, please feel free to leave me a message on my talk page.

Wikipedia:Your first article has more information about creating articles, and you may also want to read our introduction page to learn more about contributing. Thank you. Pyrrhic victor (talk) 13:04, 23 May 2026 (UTC)Reply