User talk:ProteinBoxBot

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

Files missing description details[edit]

Dear uploader: The media files you uploaded as:

are missing a description and/or other details on their image description pages. If possible, please add this information. This will help other editors make better use of the images, and they will be more informative to readers.

If you have any questions, please see Help:Image page. Thank you. Message delivered by Theo's Little Bot (opt-out) 04:31, 17 November 2013 (UTC)

Nomination of ARG2 (gene) for deletion[edit]

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)

Speedy deletion nomination of GPIHBP1 (gene)[edit]

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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.

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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)

Proposed deletion of MEMO1 (gene)[edit]

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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)

GPERAPOA1 ???[edit]

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

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)

Template:PBB/7884[edit]

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)

@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)

Redirects[edit]

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)

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)
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)
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)
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)
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)


Electron microscopy structures to be included in the box[edit]

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)

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)

Date bug[edit]

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)

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