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Gene Wiki – Discussion |
Have you noticed the Catalase page? Someone has added another identifiers template above this version. This seems crazy. Do you think its the desire for a direct link to pfam that has driven this edit? Has this been discussed anywhere else? David D. (Talk) 05:59, 5 February 2008 (UTC)
Just ran an analysis that I thought was pretty interesting… I took all 8352 PBB pages we currently have, and googled the corresponding gene symbols. In over 60% of cases, the Wikipedia gene page was shown on the front page! (Keep in mind that some gene symbols that match more common acronyms will never show up on the front page, e.g., CAT, AGT, LEP.) There’s still room to grow, but I think this is a pretty darn good start. (Obviously not all PBB's work, since many genes were preexisting, and many people have done significant work improving PBB pages...) Anyway, check out the histogram at right... Cheers, AndrewGNF ( talk) 01:29, 6 February 2008 (UTC)
Hi! The bot currently doesn't give any sources (like here); that's problematic for verifiability. Could it be instructed to add sources (perhaps also to images it previously uploaded)? -- Lea ( talk) 10:42, 8 February 2008 (UTC)
Good day. I had a look at Tumor necrosis factor receptor, and thought it might need some articles on its genes, since they're all pretty notable in immunology. Can the bot do this? Mikael Häggström ( talk) 08:39, 9 February 2008 (UTC)
Hi there.
I've been watching this for any specific replies from PDB although I've not really expected anything. The restrictions stated by PDB are very plain in meaning.
Breaking it down plainly:
Hoards of people use "public domain" according to a private interpretation and not a legal one. This is an instance. It is very clearly erroneous to label PDB images as public domain. Moreoever, PDB images simply are not free images per the Wikimedia definition of free. For what it's worth, Citizendium tags PDB images like this.
Stephen Ewen ( talk) 08:49, 6 February 2008 (UTC)
Done. Tim Vickers ( talk) 18:18, 6 February 2008 (UTC)
Thanks for uploading Image:PBB_GE_NIPA1_gnf1h07157_at_fs.png. I noticed that the file's description page currently doesn't specify who created the content, so the copyright status is unclear. If you did not create this file yourself, then you will need to specify the owner of the copyright. If you obtained it from a website, then a link to the website from which it was taken, together with a restatement of that website's terms of use of its content, is usually sufficient information. However, if the copyright holder is different from the website's publisher, then their copyright should also be acknowledged.
As well as adding the source, please add a proper copyright licensing tag if the file doesn't have one already. If you created/took the picture, audio, or video then the {{ GFDL-self}} tag can be used to release it under the GFDL. If you believe the media meets the criteria at Wikipedia:Fair use, use a tag such as {{ non-free fair use in|article name}} or one of the other tags listed at Wikipedia:Image copyright tags#Fair use. See Wikipedia:Image copyright tags for the full list of copyright tags that you can use.
If you have uploaded other files, consider checking that you have specified their source and tagged them, too. You can find a list of files you have uploaded by following this link. Unsourced and untagged images may be deleted one week after they have been tagged, as described on criteria for speedy deletion. If the image is copyrighted under a non-free license (per Wikipedia:Fair use) then the image will be deleted 48 hours after 00:02, 8 February 2008 (UTC). If you have any questions please ask them at the Media copyright questions page. Thank you. Nv8200p talk 00:02, 8 February 2008 (UTC)
Just great, let's fight to delete a diagram of gene expression but try and save an article on Corey Worthington. The priorites seem a little skewed here. David D. (Talk) 03:16, 8 February 2008 (UTC)
Hi, please have a look at [2]; the Luo et.al paper in the further reading section has a wrong doi identifier. I fixed it by hand now, but you should fix your bot too. Cheers, AxelBoldt ( talk) 21:55, 10 February 2008 (UTC)
Subject: Re: citing the pdb From: Rachel Kramer Green <kramer@rcsb.rutgers.edu> Date: Tue, 12 Feb 2008 20:48:38 -0700 To: Stephen Ewen <ewenste@bellsouth.net> CC: info@rcsb.org Dear Mr. Ewen, Thank you for your email message. Just to clarify -- our citation information is located at http://www.rcsb.org/robohelp_f/#site_navigation/citing_the_pdb.htm In particular: You *may not* collect PDB images and data and just sell the images and data commercially You *may *download the images and put them in a book (including a reference to us) and sell that commercially You *may *download the data, and do something with it, and sell that it commercially Please let us know if we can be of additional assistance. Sincerely, Rachel Green ************************** Rachel Kramer Green, Ph.D. RCSB PDB kramer@rcsb.rutgers.edu ************************** Stephen Ewen wrote: > Hello. I am trying to seek clarification on http://www.rcsb.org/pdb/static.do?p=general_information/about_pdb/contact/index.html > > Specifically the portion that states "PDB data and images from the RCSB PDB website, and may be sold, as long as the images and data are not for sale as commercial items themselves." > > May I or may I not collect PDB images and data and sell just the images and data commercial? > > Kindly advise, > > Stephen Ewen, M.Ed >
Clearly, {{ Attribution}} would also be a misleading way to tag PDB images - as I thought along. You gotta ask the questions real pointed sometimes!
Stephen Ewen ( talk) 06:23, 13 February 2008 (UTC)
It would be good to increase the number of cross-references between the gene pages such as Choline acetyltransferase and the semi-automatic enzyme pages, such as Carnitine O-octanoyltransferase. At present we have two parallel sets of pages that overlap in places. However, the enzyme pages should be broad and cover the activity in all organisms, while the gene pages cover the enzyme's gene/protein in humans.
I suggest a EC number redirect to a general enzyme page, which can be targeted by a standard field in the PBB template. This general page would have the standard enzyme name as the title eg "Carnitine O-octanoyltransferase". The human gene page would have the gene ID as its title. A "See also" section in the general enzyme page could link to "Carnitine O-octanoyltransferase in humans". Tim Vickers (talk) 19:01, 26 February 2008 (UTC)
Could the operators of this bot please review this edit that I made to CDH1 (gene)? It improves the layout of the article, eliminating the blank space that gets rendered at the top; compare [3] and [4]. Melchoir ( talk) 09:25, 6 March 2008 (UTC)
First of all, thank you for operating this excellent bot! Would it be feasible to link some or all GO terms to Wikipedia entries, as well as to the GO reference site? Not sure if one would want to do this only where an article already exists, redlink to encourage article creation, or automatically create stubs. Pseudomonas( talk) 19:48, 10 March 2008 (UTC)
This CDH1 (gene) example above... It has several representative PDB files but no pictures. It suppose to be there. 1i7w is mouse protein, but 2omv is human cadherin (chain B/2). This is probably a combination of protein chains from two different species. Could that be a reason for missing picture? Biophys ( talk) 00:01, 13 March 2008 (UTC)
Thank you for uploading Image:PBB GE PPP4R1 201594 s at tn.png. However, it currently is missing information on its copyright status. Wikipedia takes copyright very seriously. It may be deleted soon, unless we can determine the license and the source of the image. If you know this information, then you can add a copyright tag to the image description page.
If you have any questions, please feel free to ask them at the media copyright questions page. Thanks again for your cooperation. Polly ( Parrot) 21:06, 2 April 2008 (UTC)
Thank you for uploading Image:PBB GE DMTF1 203301 s at tn.png. However, it currently is missing information on its copyright status. Wikipedia takes copyright very seriously. It may be deleted soon, unless we can determine the license and the source of the image. If you know this information, then you can add a copyright tag to the image description page.
If you have any questions, please feel free to ask them at the media copyright questions page. Thanks again for your cooperation. Polly ( Parrot) 21:07, 2 April 2008 (UTC)
There is a fault with SLC47A2 -wrong name at the beginning ♦Blofeld of SPECTRE♦ $1,000,000? 17:32, 9 April 2008 (UTC)
I stumbled upon the CYP2A13 article the other day and went to wikify some words in the article and that's how I learned about this bot (which I think is great by the way). I was about to wikify some words and realized the bot would overwrite the summary with any updates. I didn't think it was necessary to make update_summary = no and make it so the article required manual inspection from then on because it wouldn't be updated. So would it be possible for the bot to automatically wikify certain words that appear in the PBB Summary after an update?
I've looked in your talk page archives and see the issue has come up before. In November 2007 you said "I think wikilinks are more valuable than incremental revisions from NCBI." Do you still think so? Are the summaries frequently updated? I noticed another user suggesting the bot check which words are currently wikilinked in an article and putting those words into a list so they will be wikified after the bot updates a summary. Do you think that's feasible?
I suppose some people would prefer humans wikify words rather than bots (so words are not overlinked). I guess the task could be performed by another editor using AutoWikiBrowser or a similar tool, although the editor would probably have to turn summary updates off. I suppose checking a wordlist may slow the bot down, but I think it would be great if the bot could automatically wikify the first instance of words like cytochrome, cholesterol, steroids, lipids, endoplasmic reticulum, nitrosamine, tobacco, etc. I appreciate your work on the bot and I will understand if you are busy with other things or don't think the idea would be workable. Thank you for your time. -- Pixelface ( talk) 21:19, 10 April 2008 (UTC)
Hey, could the maker of this bot be so kind as to include {{Wikiproject MCB|class=Start}} into the talk pages of the new articles it creates. I went through the first 500 in the ProteinBoxBot edit history and added it to those latest ones, but after noticing how many more pages of 500 there were I noticed I don't want to waste my the effort doing it manually (and am ignorant on how to make bots for tasks) when it probably is much easier for you to add that extra function to your bot (and maybe make it go back through and do similar to the new pages it had created in the past with a red "discussion" page that I was unable to get through to). 216.161.88.183 ( talk) 03:38, 13 April 2008 (UTC)
Hi. I think that the naming of articles by this bot contravenes the style guidelines. For example MAGI1 should be Membrane associated guanylate kinase, WW and PDZ domain containing 1. The same applies to all the other articles this bot created. Can it automatically move the pages to meet the guidelines? If the page already exists and is a redirect to the page that is being moved, the bot can continue the move; otherwise, human intervention would be needed. -- Seans Potato Business 16:10, 20 April 2008 (UTC)
Refer to
Template:PBB Controls. Since the template is empty and is used first thing in some articles, it is causing a lot of pages to start with an empty line, which i think makes the article look strange. I propose the use of this bot (if possible) to correct the code source of the protein articles where this happens. The solution is to start the article with the current <!-- -->
comment and, in the same line, start off the template with the {{PBB Control|...}}
command.
I'm adding this same comment on the Template:PBB Control talk page. ~ Jotomicron 15:53, 23 April 2008 (UTC)
Hi ProteinBoxBot!
We thank you for uploading
Image:PBB Protein PPARA image.jpg, but there is a problem. Your image is currently missing information on its copyright status. Wikipedia takes
copyright very seriously. Unless you can help by adding a
copyright tag, it may be
deleted by an
Administrator. If you know this information, then we urge you to add a
copyright tag to the
image description page. We apologize for this, but all images must confirm to policy on Wikipedia.
If you have any questions, please feel free to ask them at the
media copyright questions page. Thanks so much for your cooperation.
This message is from a
robot. --
John Bot III (
talk)
20:40, 24 April 2008 (UTC)
..a very nice bot by the way...thanks :-) Ivo ( talk) 05:39, 15 May 2008 (UTC)
If the bot will be making more edits, it would be appreciated if it could use an endash between page numbers, rather than a hyphen. It's causing a lot of unnecessary bot edits and would hopefully be an easy fix for you to implement! Thanks a lot. Smith609 Talk 10:44, 11 June 2008 (UTC)
A tag has been placed on Image:PBB GE PCDHB11 221408 x at tn.png requesting that it be speedily deleted from Wikipedia. This has been done under section I8 of the criteria for speedy deletion, because it is available as a bit-for-bit identical copy on the Wikimedia Commons under the same name, or all references to the image on Wikipedia have been updated to point to the title used at Commons.
If you think that this notice was placed here in error, you may contest the deletion by adding {{
hangon}}
to the top of
the page that has been nominated for deletion (just below the existing speedy deletion or "db" tag), coupled with adding a note on [[ Talk:Image:PBB GE PCDHB11 221408 x at tn.png|the talk page]] explaining your position, but be aware that once tagged for speedy deletion, if the article meets the criterion it may be deleted without delay. Please do not remove the speedy deletion tag yourself, but don't hesitate to add information to the article that would render it more in conformance with Wikipedia's policies and guidelines. Lastly, please note that if the article does get deleted, you can contact
one of these admins to request that a copy be emailed to you.
·Add§hore·
Talk/
Cont
18:43, 4 July 2008 (UTC)
the bot's template is creating an unnecesasry empty paragraph directly under the page title, this should be fixed to conform to other WP-page styles see Apolipoprotein E for example -- 213.23.255.101 ( talk) 08:12, 8 July 2008 (UTC)
Hi - I was wondering if it was possible to slow your protein box bot down a little. There are only a handful of us patrolling new templates, and I for one generally look through a whole day's worth of templates in one sitting - normally about 150 templates. Your bot has made over 3000 in the last 24 hours, making it a lot harder to get to any other new templates in the new pages lists. If it's possible for you to slow it down to, say, 40-50 an hour, it would be a big help to those of us sifting out the other templates! Grutness... wha? 01:28, 9 July 2008 (UTC)
Hi there, I edited GPI (gene) a bit, but since there is no bot control template on the page any more, I wasn't sure if these changes will remain. I added the template myself manually, which I hope is what you need to do. However, finding and adding a template is probably beyond the capabilities of newbies, so although the new arrangement is cleaner, I think we still need to include this control template by default. Tim Vickers ( talk) 16:13, 9 July 2008 (UTC)
Hadn't noticed it! If you change the hidden text to "To stop automatic updates of the summary text change the update_summary field to "no" in the Template:PBB_Controls at the bottom of the page ." that is a bit more explicit. Tim Vickers ( talk) 17:55, 9 July 2008 (UTC)
Then we'll need to add text telling people to remove everything apart from the PBB template at the top. We need to make this as newbie-proof and approachable as possible. Tim Vickers ( talk) 20:37, 9 July 2008 (UTC)
Hello,
You have included this picture inside Category:Copyright holder released public domain images. However, the introductory statement at the top of that category says : "Please include all evidence you have that creator desires the image to be public domain on the image description page". Do you have any such statement that might be included in the image's description page ? Teofilo talk 13:38, 8 July 2008 (UTC)
The Ortholog section of the genes I've looked at ( such as ITK_(gene) ) list coordinates on mm8 at http://genome.ucsc.edu but the default at ucsc is mm9 ( until you visit and switch to another build ). Adding the db parameter to the url would solve this, it's &db=mm8 in the ones I've checked. PTGS2 is another example, the differences betwixt mm8 and mm9 have shifted it out of the browser window on mm9 —Preceding unsigned comment added by 198.129.91.135 ( talk) 00:56, 9 July 2008 (UTC)
I was just editing the C3orf58 page. I wanted to indicate that it may be regulated by MEF2 as the paper states. I tried to create a link to MEF2 and there wasn't one. But I realized there was a link to Mef2. So I used that.
However, Mef2 may not be human--that's a Drosophila symbol, it appears. And that page has 4 genes on it that appear to be the human ones. But they aren't MEF2, they are MEF2A, MEF2B, MEF2C, and MEF2D.
Not sure how to handle that. —Preceding unsigned comment added by Mary Mangan ( talk • contribs) 20:19, 11 July 2008 (UTC)
Ooops, I made this edit thinking I had a solution, but clearly the issue is deeper than that (as discussed here). Gotta run now, but feel free to undo any of what I did... Cheers, AndrewGNF ( talk) 02:11, 12 July 2008 (UTC)
Hi! I've noticed that some images uploaded by this bot, like Image:PBB GE FREM2 gnf1h07842 at tn.png or Image:PBB_GE_FREM2_gnf1h07842_at_fs.png, are in PNG format. Besides that all these images should be better uploaded into the Wikimedia Commons to be shared among all the different Wikipedias (and put into an adequate category there), I'd like to raise your attention about the following policy: Use SVG over PNG (and [7]). The SVG format is much more appropriate for this kind of images, offering more flexibility, more image quality and space efficiency, and the MediaWiki software ensures compatibility with all browsers. Thanks! — surueña 08:20, 11 July 2008 (UTC)
Hello folks--I've been trying to make some edits learn the ropes, and there are a few things that I thought I would add to the discussion. Feel free to edit/move/disregard/whatever.
1. It would have helped me if there was a box on the gene pages that pointed to the project goals, guidelines, templates, situations for new genes, etc. I had to sift through a bunch of different documentation to try to figure out what to do. And ask questions on the our blog and in the talk pages. Maybe there is some central location/forum (like here?), but I don’t know where it is or how to locate that. I guess I’m asking for a contributors’ forum or something?
2. The new gene creator template is helpful, but what would really help me is to have a whole mock page to simply copy/paste that had the right sections: a discussion section (and some lorem ipsum text is fine), and then some mock references all formatted right, subsections, and the box creator. I kinda tried to do that with the Map4 page, but that didn’t work out very well.
3. I have to advocate for some training…ok, that’s my job probably…but I think there are some people out there who would contribute if you could create a community around it with some support and some carrots (still not sure what the carrots are yet). Retired scientists, stay at home parents with science training, hobbyists, family members with genetic issues, in addition to the practicing scientists and students. But there needs to be some outreach and wrangling there.
Mary Mangan ( talk) 17:37, 11 July 2008 (UTC)
New comment: Is the Gene Wiki project the same thing as the Wikipedia:WikiProject_Molecular_and_Cellular_Biology one, as the box on the Talk:MAP4 page shows now? I went over to MCB to understand that better, but it isn't clear to me if it is part of the same thing. —Preceding unsigned comment added by Mary Mangan ( talk • contribs) 17:58, 12 July 2008 (UTC)
PBB links to UCSC for mitochondrial (MT) genes is not happening. See ND6, COX2 and the location links. The display looks like you'll get something at UCSC, but you won't. Needs to be chrM. There's some other oddness about the M genes, but I can't quite figure out what that is yet. Mary Mangan ( talk) 00:10, 12 July 2008 (UTC)
Dear Sirs, may I ask you four questions:
Yours faithfully, Simplicius, Germany
It would be useful to provide editors an easy way to edit the PBB template page, for example to replace the protein struture graphic, add missing EC numbers, etc. This can be accomplished rather ineligantly using the following syntax:
This places a small hyperlink labeled "edit" above the PBB box in the article. This solution is not ideal since (1) the syntax is rather messy and detracts from the simplification of using PBB template and (2) the hyperlink is placed above rather than in the template. A much better solution would be to add this functionity directly in the template rather than as a parameter to the template. Boghog2 ( talk) 17:48, 24 July 2008 (UTC)
e.g. with the wikilinks in this edit: http://en.wikipedia.org/?title=MAGEA3&diff=227790302&oldid=224566405 be reverted when the summary is updated? Thanks, -- Rajah ( talk) 07:50, 25 July 2008 (UTC)
I am kind of wondering at the utility of the protein boxes. Here are some basic questions I have. I noticed that on the HLA-DQA1 and HLA-DQB1 page it showed (I changed the name) a picture of HLA-DQ and called it HLA-DQA1, the same was true for HLA-DQB1. On the HLA-DR page it has a HLA-DRA gene and a picture of an HLA-DR molecule. Also in error it claims there are no mouse homologs, the homolog for HLA-DQ in mice is MHC-IA, so that bit of information is also wrong. The repository for HLA sequence information is IMGT/EBI, not pubmed, so it is much better to have a protein box that uses IMGT/EBI as a source of information. The final issue is it displays a list of images but some of these images are minor variations used as a part of single studies. Even for someone who has created pages on all the HLA-A and HLA-B, I think that so much information is a waste, its like having a full author list when author1, author2, author3, et al. will do. In addition the box contains three graphs with essentially the same information whereas it has been known since 1970 and is listed in the DR, DQ and DP pages that these antigens are found on lymphoid tissues. The protein box extract placed as the lead paragraph is not wikified and cannot be wikified. I can go on. What is the benefit of doing this if it simply throws trivia onto pages? Also if a person finds an error in the box and corrects it, the next update will override the correction, probably with the same incorrect information. That process overrides expert review of materials. PB666 yap 05:21, 27 July 2008 (UTC)
Thanks guys for sorting this all out. The pages look great. I gotta admit, I'm a bit glad I was late to this party. Longstanding confusion from my days as an undergrad leaves antigen presentation (and adapative immunity, in general) as one of my carefully nurtured areas of ignorance. ;) AndrewGNF ( talk) 17:23, 28 July 2008 (UTC)
Thank you for uploading Image:PBB Protein NFAT5 image.jpg. However, it currently is missing information on its copyright status. Wikipedia takes copyright very seriously. It may be deleted soon, unless we can determine the license and the source of the image. If you know this information, then you can add a copyright tag to the image description page.
If you have uploaded other files, consider checking that you have specified their license and tagged them, too. You can find a list of files you have uploaded by following this link.
If you have any questions, please feel free to ask them at the media copyright questions page. Thanks again for your cooperation. Sdrtirs ( talk) 16:13, 14 August 2008 (UTC)
Thank you for uploading Image:PBB GE TLK2 212986 s at fs.png. However, it currently is missing information on its copyright status. Wikipedia takes copyright very seriously. It may be deleted soon, unless we can determine the license and the source of the image. If you know this information, then you can add a copyright tag to the image description page.
If you have uploaded other files, consider checking that you have specified their license and tagged them, too. You can find a list of files you have uploaded by following this link.
If you have any questions, please feel free to ask them at the media copyright questions page. Thanks again for your cooperation. Sdrtirs ( talk) 16:15, 14 August 2008 (UTC)
Hi! Could I copy the contents of the protein box, for example, from the NOTCH1 when I create a page in the Russian Wiki? If yes, how do I do this? Thanx. -- CopperKettle ( talk) 04:37, 19 August 2008 (UTC)
Your bot has uploaded hundreds of duplicate images. One example:
Was this intentional? And if so, what can we do to eliminate these duplicates? Image redirects now work. So perhaps for a case like this, the image could be re-uploaded as Image:PBB_Protein_PUM_image.jpg and then delete the files at PUM1 and PUM2 and make them redirects? Let me know your thoughts. One thing that's clear is that having all of these duplicates is not a good situation. -- MZMcBride ( talk) 02:28, 15 September 2008 (UTC)
Obviously there is a difference between proteins and genes. Why are there hundreds of pages (e.g. GPR3) that incorrectly state that so-and-so protein is a "human gene"? Perhaps the protein and the gene that codes for it have similar names, but that is no reason to conflate the two. It would be absurd to go through and correct all the articles with this error. Perhaps a bot could do it? Fuzzform ( talk) 00:03, 2 October 2008 (UTC)
Sorry, traveling this week, but will reply as soon as I get a chance... Just didn't want anyone to think they were being ignored (especially when they come offering to participate!) AndrewGNF ( talk) 06:44, 9 October 2008 (UTC)
Hello AndrewGNF. Thank you for uploading the Gene expression pattern diagrams. I would like to ask you for uploading the images in future on Wikimedia Commons. Then other Wikis are able to use the images, too. Thanks a lot! Regards, -- Bcr-abl ( talk) 10:22, 7 October 2008 (UTC)
Hi Andrew, is there any way the bot could check for alternate names for a gene/protein before it goes ahead and creates an article? I've been trying to link up all the tyrosine kinase articles. I keep coming across articles that have been created by the bot, were an article already exists under the proteins alternate name, see NTRK3 and TrkC, I'll leave these as they are for now as an example. K.murphy ( talk) 13:54, 10 November 2008 (UTC)
If a protein summary contains a technical term that should be linked to its Wikipedia article but isn't, what is the correct way to proceed? Please document this at the relevant template pages. Thanks, AxelBoldt ( talk) 00:39, 31 December 2008 (UTC)
I am trying to built up a portal using two templates to make it a bit easier. The elements of each page can be changed quite easily. What elements are needed? Please feel free to do changes and to fill the elements with contents. Simplicius ( talk) 16:57, 30 July 2008 (UTC)
I think we absolutely want to maintain and emphasize our connection with WP:MCB. How should we do this? In my mind, this portal will serve two purposes. First (and most obviously), an organizational hub for people who want to focus on gene and protein annotation. Second, I hope many people come to edit the gene wiki through past and upcoming press -- and these newbies will be true novices. I hope this portal is a gentle landing point for those people... AndrewGNF ( talk) 01:10, 1 August 2008 (UTC)
The portal uses two templates to generate new paragraphs:
Thx! Simplicius ( talk) 12:48, 6 August 2008 (UTC)
Andrew, (no critics, just a question) why do you prefer an [edit]-function via web address instead of wiki link? Simplicius ( talk) 13:41, 6 August 2008 (UTC)
Please use this template for some "advertisment".
About the portal, please develope the primal questions for interested users:
You started already. Please go on.
And please try to put the works' output (WP articles etc.) onto the first page portal as an entertaining and informing page, and the technical hints and helps onto the second page Gene Wiki – Facilities. Simplicius ( talk) 14:00, 6 August 2008 (UTC)
I will try to find the tools for supervising articles in a category so that you can see changes automatically. Please allow me a question: is there are certain category for articles generated by this project or by your tools? -- Simplicius ( talk) 13:41, 6 August 2008 (UTC)
Link - very cool. Tim Vickers ( talk) 02:19, 4 September 2008 (UTC)
I know there is an article now, which is great, but what happened to the nice description and images like these: Image:PBB_flowchart.png, Image:PBB_flowchart_Sub.png? It would be really great to have an updated, detailed article. -- Dan| (talk) 14:07, 4 November 2008 (UTC)
I found this page via "PLoS Biology - Metagenome Annotation Using a Distributed Grid of Undergraduate Students".. After half an hour I still have no idea from this page how I may begin to annotate. Is this not a lack in a basic purpose of the page? Mccready ( talk) 01:36, 26 November 2008 (UTC)
Dear Mr. or Ms. Bot: The double-column format for Further Reading does not look so good on my computer. The single-column format at ST3GAL3 looks much better. Can you fix yourself so you output the Further Readings in single column? Sincerely, your friend, GeorgeLouis ( talk) 05:08, 30 April 2009 (UTC)
Yes, it looks very nice. GeorgeLouis ( talk) 17:55, 30 April 2009 (UTC)
Does anyone happen to remember where our last discussion of the lead sentence of PBB articles is? The best I can find is in User_talk:ProteinBoxBot/Archive2#Protein_vs._Gene, but somehow I seem to remember a more detailed discussion with several options. Hoping someone else's memory is better than mine... Cheers, AndrewGNF ( talk) 18:09, 30 April 2009 (UTC)
Is is possible for PBB to include wikilinks in the summaries it provides using the PBB_Summary tempalte? For example, TNFRSF21 would benefit from several wikilinks. Most articles in PBB's scope probably have similar stub-like articles, with a brief lead having one or two wikilinks to general terms, and then a paragraph from PBB that has some specific terms that are obscure to a typical reader. In the TNFRSF21, for example, NF-kappaB, MAPK8/ JNK, TRADD are meaningless to almost everyone outside of molecular biology. And the following terms are probably meaningless to most people outside of general biology: TNF-receptor, apoptosis, domain, receptor, signal transduction, knockout, T-helper cell.
I suppose it might be difficult to have PBB identify which terms should be linked, whether that term has a corresponding Wikipedia article, and whether the article matching that term is actually about the intended topic (a link to " knockout", for example, would lead to something other than knockout gene). — Twas Now ( talk • contribs • e-mail ) 10:22, 24 May 2009 (UTC)
[[TRADD]]
; when it comes across "JNK", it will change it to [[c-Jun N-terminal kinases|JNK]]
. Ambiguous terms should generally not be added to the whitelist. For example, if PBB comes across "knockout" but not "knockout gene", there is a slight (...very slight) chance it might mean a literal
knockout, and not
knockout gene. There are more plausible examples, with subtler ambiguity, but I already used this one above... in reality, it would probably be fine to link
knockout gene in all cases. —
Twas Now (
talk •
contribs •
e-mail )
18:04, 24 May 2009 (UTC)Anyone watching here might be interested in this topic: Wikipedia_talk:WikiProject_Molecular_and_Cellular_Biology#Relating_gene_pages_by_protein_interactions. Cheers, AndrewGNF ( talk) 22:47, 25 June 2009 (UTC)
For anyone concerned Protein Box Bot will be making some page edits soon. See the announcement here. JonSDSUGrad ( talk) 00:21, 23 July 2009 (UTC)
Two more that I found and reverted, just for the record... [16] and [17] AndrewGNF ( talk) 03:00, 28 July 2009 (UTC)
A request for comment has been made at the above link. Your input is welcome. Boghog2 ( talk) 20:32, 19 August 2009 (UTC)
We've created the version 0.1 tool for generating a Gene Wiki page on demand, modeled after Diberri's template filler. It's hooked up to our BioGPS application, accessible at http://biogps.gnf.org. So that the default output is focused on the GeneWikiGenerator tool, most users here will be interested in using this URL: http://biogps.gnf.org/GeneWikiGenerator/. From there, search for your favorite gene by most public identifiers, symbols or aliases (or try one of the example queries), and then select one of the returned genes in the left-hand "Current gene list". You'll then see two windows. The bottom one has the Wikipedia page for the gene, if one exists. The top one has the wikitext and instructions for creating or updating a gene page according to the standard "Gene Wiki" format. If people here have a chance to try it out, we'd love to hear feedback.
(As a plug for BioGPS more generally, you can see the other gene report views by changing the "current layout" in the upper right. If you register for a free user account, you can further customize your layouts by mixing and matching any of the 150+ plugins in the plugin library. Any comments on BioGPS in general are also welcome... </shameless_plug>) Cheers, AndrewGNF ( talk) 00:11, 27 August 2009 (UTC)
Hi Tim. Thank for all your excellent work. Did somebody go through all the human gene locations and edit out the locations? It seems as though they used to list gene location using the old cytogenetic band tags (like "15p2.23") Next they seemed to change to a numeric address expressed in megabasepairs (which I suppose they needed to abandon because there is so much intervariability in humans....like the variable region of triplet repeats that result in fragile- X syndrome). But "n/a" is not useful. At least the old cytogenetic terminology could get you in the ball park. Last year I built a large map that labels the cytogenetic bands, and there is an approximate scale so that users could at least get close to locating what they were looking for. If we're ever going to understand the architecture of the genome, we'll need to create tools to help us see the relationships (Entrez Gene is OK, but it's so "all-inclusive" that it's hard to find anything.) Tim, I'd like to help, but I'm not sure where to start. doctorwolfie ( talk) 14:16, 4 September 2009 (UTC)
I'm looking for some examples of edits to gene pages and I'm hoping people watching here might have suggestions. I want to highlight one (or ideally a handful) of edits that satisfy these two criteria: 1) includes a citation to a scientific reference, and 2) adds information that could be expressed as a Gene Ontology annotation but hasn't been done so by the annotation authorities. For example:
Hmmm, I guess not terribly hard to find, but perhaps people here have particularly good examples to highlight? Cheers, AndrewGNF ( talk) 01:32, 9 September 2009 (UTC)
I am an author of the German wikipedia and also edit sometimes in the English wikipedia, mainly on biochemistry articles. I have been active on some gene articles and I noticed that the GNF Protein box and the GNF Ortholog box templates have a lot of useful links to other databases but these mainly cover single genes or gene products (like Entrez, Ensembl and Uniprot) but a link to a phylogenetic database is not present. So I felt that there would be a lot of added value if there were a direct link to a phylogenetic database that lists orthologs of a specific gene. This would allow the exploration of its corresponding genes in hundreds of complete genomes. There are already links from Uniprot to phylogenetic databases but you have to scroll all the way down to find them.
I am currently working with a group at ETH that created the OMA-database ( http://www.omabrowser.org). It is one of the biggest orthology databases and many other website such as Uniprot and Ensembl link to OMA. Since I know this project best I would suggest to integrate this website into the GNF Protein box but there are also other projects which might be more suited for Wikipedia. On the technical side, the change in the infobox would only consist of a small adjustment since the database could be called directly with the uniprot entry ID (e.g. http://www.omabrowser.com/cgi-bin/gateway.pl?f=DisplayEntry&p1=PROCA02187 in the case of OMA). Did you discuss such an idea already? What do you think? Greetings -- hroest 12:07, 9 September 2009 (UTC)
As discussed previously, there is a consensus to change the lead sentence to make clear that Gene Wiki pages are about both the gene and the protein encoded by that gene. The consensus reached was that the opening sentence (using GPR3 as an example) should read as follows:
Perhaps this should be modified slightly according to this as follows (replacing "which" with "that" is probably a good idea although the additional two commas in my opinion is over doing it):
In addition, the name should probably be taken from the UniProt database (protein name) rather than HUGO (gene name) while the gene symbol would be as before (i.e., the HUGO gene symbol). The UniProt protein name is often the same as the HUGO name, but sometimes differ (compare for example estrogen receptor beta where the UniProt name is "estrogen receptor beta" while the HUGO name is "estrogen receptor 2 (ER beta)".
Given the never ending controversy that this opening sentence has generated, I would like BogBot to get started on this in near future. I think it will be straight forward to write a regular expression that will recognize and replace the existing boiler plate lead sentence and leave untouched any sentence that a human editor has modified.
Thoughts concerning the two minor changes proposed above? Also how best to proceed (bring this up again with the MCB project followed by WP:Bots/Requests for approval)?. Cheers. Boghog ( talk) 13:53, 27 September 2009 (UTC)
Following a discussion here, I've written a draft program which takes in a PDB ID and outputs a ray traced image of the corresponding structure. When I enter standard commands to make the image's background transparent in PyMOL (using version 0.99r6 on Windows), however, I can't seem to make them work. Specifically, entering 'set ray_opaque_background, 0' and/or 'set opaque_background, 0' does not result in the expected checkerboard background indicating a transparent background (see a relevant entry in PyMOLWiki here: http://pymolwiki.org/index.php/Ray_opaque_background). Using the GUI to select 'Display' -> 'Background' and uncheck 'Opaque' and then check 'Show Alpha Checkerboard' does nothing. This is odd, because I've made backgrounds transparent in PyMOL before (see [25], [26]). Has anybody run into a similar problem? Trouble-shooting via Google hasn't helped. Emw2012 ( talk) 14:10, 27 September 2009 (UTC)
(unindent) I think I may have found a workaround to the cropping issue by using GIMP -- simply autocrop the image and add some fixed number of pixels (e.g., 25) as padding. Presumably this will be the solution once I find out how to incorporate the simple process for the fix into a batch script. However, while the image itself looks good, it seems to be deformed once its added to the 'GNF Protein box' template. The problem is viewable at User:Emw/PDBImageTestcases_2. Any ideas on what may be causing this? Emw ( talk) 00:51, 15 November 2009 (UTC)
Has the SCOP classification feature of the 'Automate PDB uploads' project proposal been implemented ( Portal:Gene_Wiki/Project_proposals#Automate_uploads_of_PDB_images)? The automation needed to implement the SCOP feature seems straightforward in concept: go to the SCOP website, enter the PDB ID of interest into the search form, and parse from the retrieved lineage any elements of interest.
Which elements of a SCOP lineage should be retrieved by the feature (e.g., class, fold, superfamily, family, protein, and/or species)? And where should the information on the elements be put -- somewhere as a new field in one of the templates used by ProteinBoxBot, and/or in a newly added 'Summary' box in the image file itself (e.g. File:PBB_Protein_MMP9_image.jpg)? Emw ( talk) 16:12, 4 November 2009 (UTC)
Typically, gene articles containing protein structure images are titled in the form <HUGO symbol> (e.g. MMP9) or <HUGO symbol>_(gene) (e.g. PIR (gene)). Of the 2774 articles having structure images, there are about 221 that don't follow either of those two naming conventions. For example, consider interleukin 6, with the HUGO gene symbol IL6 -- IL6 is a disambiguation page and IL6 (gene) doesn't currently exist. Would it make sense to add IL6 (gene) as a redirect for this article, and to apply this pattern to the roughly 10% of gene articles with structure images that are not accessible via HUGO gene symbol? Emw ( talk) 21:31, 24 December 2009 (UTC)
Hi folks, I'm looking at merging all the different Telomerase RNA component articles that WP has amassed. At the top of the page is an odd phrase 'n/a (protein)n/a (protein)'. I suspect this is coming from the 'PBB|geneid=7012' template. I guess something in the template is spitting the dummy because this is not actually a protein. Is there a quick fix?-- Paul ( talk) 08:09, 9 October 2009 (UTC)
Is integrin α4β7 (called LPAM-1, lymphocyte Peyer's patch adhesion molecule 1, here) the same as ITGB7? And while I am at it: Alpha-v beta-3 is probably the same as a ProteinBoxBot-created article, but which? -- ἀνυπόδητος ( talk) 11:04, 14 October 2009 (UTC)
According to WHO, glycoprotein 72 is the target of several monoclonal antibodies ( anatumomab mafenatox, minretumomab, indium (111In) satumomab pendetide). It seems to be the same as CA 72-4, but I'd like to be sure before I create a redirect. Can anybody help? -- ἀνυπόδητος ( talk) 18:50, 24 October 2009 (UTC)
The image is actually of HuC (ELAVL-3), not HuD (ELAVL-4). Only two structures exist in the PDB, both RNA-bound dimers. These are 1FXL and 1G2E. regards, Sunil060902 ( talk) 17:17, 27 October 2009 (UTC)
The Bot that does the protein images added the full chemical name of titin, a ridiculous amount of characters, could this be fixed? -- The New Mikemoral ♪♫ 06:12, 16 November 2009 (UTC)
BogBot changed the bolded name of this protein so it doesn't match the article title any more. It should be merged with EpCAM anyway, but in which direction? And how is this done without breaking the {{ PBB Summary}}? -- ἀνυπόδητος ( talk) 12:36, 16 November 2009 (UTC)
![]() | This is an archive of past discussions. Do not edit the contents of this page. If you wish to start a new discussion or revive an old one, please do so on the current talk page. |
Archive 1 | Archive 2 | Archive 3 | Archive 4 |
Gene Wiki – Discussion |
Have you noticed the Catalase page? Someone has added another identifiers template above this version. This seems crazy. Do you think its the desire for a direct link to pfam that has driven this edit? Has this been discussed anywhere else? David D. (Talk) 05:59, 5 February 2008 (UTC)
Just ran an analysis that I thought was pretty interesting… I took all 8352 PBB pages we currently have, and googled the corresponding gene symbols. In over 60% of cases, the Wikipedia gene page was shown on the front page! (Keep in mind that some gene symbols that match more common acronyms will never show up on the front page, e.g., CAT, AGT, LEP.) There’s still room to grow, but I think this is a pretty darn good start. (Obviously not all PBB's work, since many genes were preexisting, and many people have done significant work improving PBB pages...) Anyway, check out the histogram at right... Cheers, AndrewGNF ( talk) 01:29, 6 February 2008 (UTC)
Hi! The bot currently doesn't give any sources (like here); that's problematic for verifiability. Could it be instructed to add sources (perhaps also to images it previously uploaded)? -- Lea ( talk) 10:42, 8 February 2008 (UTC)
Good day. I had a look at Tumor necrosis factor receptor, and thought it might need some articles on its genes, since they're all pretty notable in immunology. Can the bot do this? Mikael Häggström ( talk) 08:39, 9 February 2008 (UTC)
Hi there.
I've been watching this for any specific replies from PDB although I've not really expected anything. The restrictions stated by PDB are very plain in meaning.
Breaking it down plainly:
Hoards of people use "public domain" according to a private interpretation and not a legal one. This is an instance. It is very clearly erroneous to label PDB images as public domain. Moreoever, PDB images simply are not free images per the Wikimedia definition of free. For what it's worth, Citizendium tags PDB images like this.
Stephen Ewen ( talk) 08:49, 6 February 2008 (UTC)
Done. Tim Vickers ( talk) 18:18, 6 February 2008 (UTC)
Thanks for uploading Image:PBB_GE_NIPA1_gnf1h07157_at_fs.png. I noticed that the file's description page currently doesn't specify who created the content, so the copyright status is unclear. If you did not create this file yourself, then you will need to specify the owner of the copyright. If you obtained it from a website, then a link to the website from which it was taken, together with a restatement of that website's terms of use of its content, is usually sufficient information. However, if the copyright holder is different from the website's publisher, then their copyright should also be acknowledged.
As well as adding the source, please add a proper copyright licensing tag if the file doesn't have one already. If you created/took the picture, audio, or video then the {{ GFDL-self}} tag can be used to release it under the GFDL. If you believe the media meets the criteria at Wikipedia:Fair use, use a tag such as {{ non-free fair use in|article name}} or one of the other tags listed at Wikipedia:Image copyright tags#Fair use. See Wikipedia:Image copyright tags for the full list of copyright tags that you can use.
If you have uploaded other files, consider checking that you have specified their source and tagged them, too. You can find a list of files you have uploaded by following this link. Unsourced and untagged images may be deleted one week after they have been tagged, as described on criteria for speedy deletion. If the image is copyrighted under a non-free license (per Wikipedia:Fair use) then the image will be deleted 48 hours after 00:02, 8 February 2008 (UTC). If you have any questions please ask them at the Media copyright questions page. Thank you. Nv8200p talk 00:02, 8 February 2008 (UTC)
Just great, let's fight to delete a diagram of gene expression but try and save an article on Corey Worthington. The priorites seem a little skewed here. David D. (Talk) 03:16, 8 February 2008 (UTC)
Hi, please have a look at [2]; the Luo et.al paper in the further reading section has a wrong doi identifier. I fixed it by hand now, but you should fix your bot too. Cheers, AxelBoldt ( talk) 21:55, 10 February 2008 (UTC)
Subject: Re: citing the pdb From: Rachel Kramer Green <kramer@rcsb.rutgers.edu> Date: Tue, 12 Feb 2008 20:48:38 -0700 To: Stephen Ewen <ewenste@bellsouth.net> CC: info@rcsb.org Dear Mr. Ewen, Thank you for your email message. Just to clarify -- our citation information is located at http://www.rcsb.org/robohelp_f/#site_navigation/citing_the_pdb.htm In particular: You *may not* collect PDB images and data and just sell the images and data commercially You *may *download the images and put them in a book (including a reference to us) and sell that commercially You *may *download the data, and do something with it, and sell that it commercially Please let us know if we can be of additional assistance. Sincerely, Rachel Green ************************** Rachel Kramer Green, Ph.D. RCSB PDB kramer@rcsb.rutgers.edu ************************** Stephen Ewen wrote: > Hello. I am trying to seek clarification on http://www.rcsb.org/pdb/static.do?p=general_information/about_pdb/contact/index.html > > Specifically the portion that states "PDB data and images from the RCSB PDB website, and may be sold, as long as the images and data are not for sale as commercial items themselves." > > May I or may I not collect PDB images and data and sell just the images and data commercial? > > Kindly advise, > > Stephen Ewen, M.Ed >
Clearly, {{ Attribution}} would also be a misleading way to tag PDB images - as I thought along. You gotta ask the questions real pointed sometimes!
Stephen Ewen ( talk) 06:23, 13 February 2008 (UTC)
It would be good to increase the number of cross-references between the gene pages such as Choline acetyltransferase and the semi-automatic enzyme pages, such as Carnitine O-octanoyltransferase. At present we have two parallel sets of pages that overlap in places. However, the enzyme pages should be broad and cover the activity in all organisms, while the gene pages cover the enzyme's gene/protein in humans.
I suggest a EC number redirect to a general enzyme page, which can be targeted by a standard field in the PBB template. This general page would have the standard enzyme name as the title eg "Carnitine O-octanoyltransferase". The human gene page would have the gene ID as its title. A "See also" section in the general enzyme page could link to "Carnitine O-octanoyltransferase in humans". Tim Vickers (talk) 19:01, 26 February 2008 (UTC)
Could the operators of this bot please review this edit that I made to CDH1 (gene)? It improves the layout of the article, eliminating the blank space that gets rendered at the top; compare [3] and [4]. Melchoir ( talk) 09:25, 6 March 2008 (UTC)
First of all, thank you for operating this excellent bot! Would it be feasible to link some or all GO terms to Wikipedia entries, as well as to the GO reference site? Not sure if one would want to do this only where an article already exists, redlink to encourage article creation, or automatically create stubs. Pseudomonas( talk) 19:48, 10 March 2008 (UTC)
This CDH1 (gene) example above... It has several representative PDB files but no pictures. It suppose to be there. 1i7w is mouse protein, but 2omv is human cadherin (chain B/2). This is probably a combination of protein chains from two different species. Could that be a reason for missing picture? Biophys ( talk) 00:01, 13 March 2008 (UTC)
Thank you for uploading Image:PBB GE PPP4R1 201594 s at tn.png. However, it currently is missing information on its copyright status. Wikipedia takes copyright very seriously. It may be deleted soon, unless we can determine the license and the source of the image. If you know this information, then you can add a copyright tag to the image description page.
If you have any questions, please feel free to ask them at the media copyright questions page. Thanks again for your cooperation. Polly ( Parrot) 21:06, 2 April 2008 (UTC)
Thank you for uploading Image:PBB GE DMTF1 203301 s at tn.png. However, it currently is missing information on its copyright status. Wikipedia takes copyright very seriously. It may be deleted soon, unless we can determine the license and the source of the image. If you know this information, then you can add a copyright tag to the image description page.
If you have any questions, please feel free to ask them at the media copyright questions page. Thanks again for your cooperation. Polly ( Parrot) 21:07, 2 April 2008 (UTC)
There is a fault with SLC47A2 -wrong name at the beginning ♦Blofeld of SPECTRE♦ $1,000,000? 17:32, 9 April 2008 (UTC)
I stumbled upon the CYP2A13 article the other day and went to wikify some words in the article and that's how I learned about this bot (which I think is great by the way). I was about to wikify some words and realized the bot would overwrite the summary with any updates. I didn't think it was necessary to make update_summary = no and make it so the article required manual inspection from then on because it wouldn't be updated. So would it be possible for the bot to automatically wikify certain words that appear in the PBB Summary after an update?
I've looked in your talk page archives and see the issue has come up before. In November 2007 you said "I think wikilinks are more valuable than incremental revisions from NCBI." Do you still think so? Are the summaries frequently updated? I noticed another user suggesting the bot check which words are currently wikilinked in an article and putting those words into a list so they will be wikified after the bot updates a summary. Do you think that's feasible?
I suppose some people would prefer humans wikify words rather than bots (so words are not overlinked). I guess the task could be performed by another editor using AutoWikiBrowser or a similar tool, although the editor would probably have to turn summary updates off. I suppose checking a wordlist may slow the bot down, but I think it would be great if the bot could automatically wikify the first instance of words like cytochrome, cholesterol, steroids, lipids, endoplasmic reticulum, nitrosamine, tobacco, etc. I appreciate your work on the bot and I will understand if you are busy with other things or don't think the idea would be workable. Thank you for your time. -- Pixelface ( talk) 21:19, 10 April 2008 (UTC)
Hey, could the maker of this bot be so kind as to include {{Wikiproject MCB|class=Start}} into the talk pages of the new articles it creates. I went through the first 500 in the ProteinBoxBot edit history and added it to those latest ones, but after noticing how many more pages of 500 there were I noticed I don't want to waste my the effort doing it manually (and am ignorant on how to make bots for tasks) when it probably is much easier for you to add that extra function to your bot (and maybe make it go back through and do similar to the new pages it had created in the past with a red "discussion" page that I was unable to get through to). 216.161.88.183 ( talk) 03:38, 13 April 2008 (UTC)
Hi. I think that the naming of articles by this bot contravenes the style guidelines. For example MAGI1 should be Membrane associated guanylate kinase, WW and PDZ domain containing 1. The same applies to all the other articles this bot created. Can it automatically move the pages to meet the guidelines? If the page already exists and is a redirect to the page that is being moved, the bot can continue the move; otherwise, human intervention would be needed. -- Seans Potato Business 16:10, 20 April 2008 (UTC)
Refer to
Template:PBB Controls. Since the template is empty and is used first thing in some articles, it is causing a lot of pages to start with an empty line, which i think makes the article look strange. I propose the use of this bot (if possible) to correct the code source of the protein articles where this happens. The solution is to start the article with the current <!-- -->
comment and, in the same line, start off the template with the {{PBB Control|...}}
command.
I'm adding this same comment on the Template:PBB Control talk page. ~ Jotomicron 15:53, 23 April 2008 (UTC)
Hi ProteinBoxBot!
We thank you for uploading
Image:PBB Protein PPARA image.jpg, but there is a problem. Your image is currently missing information on its copyright status. Wikipedia takes
copyright very seriously. Unless you can help by adding a
copyright tag, it may be
deleted by an
Administrator. If you know this information, then we urge you to add a
copyright tag to the
image description page. We apologize for this, but all images must confirm to policy on Wikipedia.
If you have any questions, please feel free to ask them at the
media copyright questions page. Thanks so much for your cooperation.
This message is from a
robot. --
John Bot III (
talk)
20:40, 24 April 2008 (UTC)
..a very nice bot by the way...thanks :-) Ivo ( talk) 05:39, 15 May 2008 (UTC)
If the bot will be making more edits, it would be appreciated if it could use an endash between page numbers, rather than a hyphen. It's causing a lot of unnecessary bot edits and would hopefully be an easy fix for you to implement! Thanks a lot. Smith609 Talk 10:44, 11 June 2008 (UTC)
A tag has been placed on Image:PBB GE PCDHB11 221408 x at tn.png requesting that it be speedily deleted from Wikipedia. This has been done under section I8 of the criteria for speedy deletion, because it is available as a bit-for-bit identical copy on the Wikimedia Commons under the same name, or all references to the image on Wikipedia have been updated to point to the title used at Commons.
If you think that this notice was placed here in error, you may contest the deletion by adding {{
hangon}}
to the top of
the page that has been nominated for deletion (just below the existing speedy deletion or "db" tag), coupled with adding a note on [[ Talk:Image:PBB GE PCDHB11 221408 x at tn.png|the talk page]] explaining your position, but be aware that once tagged for speedy deletion, if the article meets the criterion it may be deleted without delay. Please do not remove the speedy deletion tag yourself, but don't hesitate to add information to the article that would render it more in conformance with Wikipedia's policies and guidelines. Lastly, please note that if the article does get deleted, you can contact
one of these admins to request that a copy be emailed to you.
·Add§hore·
Talk/
Cont
18:43, 4 July 2008 (UTC)
the bot's template is creating an unnecesasry empty paragraph directly under the page title, this should be fixed to conform to other WP-page styles see Apolipoprotein E for example -- 213.23.255.101 ( talk) 08:12, 8 July 2008 (UTC)
Hi - I was wondering if it was possible to slow your protein box bot down a little. There are only a handful of us patrolling new templates, and I for one generally look through a whole day's worth of templates in one sitting - normally about 150 templates. Your bot has made over 3000 in the last 24 hours, making it a lot harder to get to any other new templates in the new pages lists. If it's possible for you to slow it down to, say, 40-50 an hour, it would be a big help to those of us sifting out the other templates! Grutness... wha? 01:28, 9 July 2008 (UTC)
Hi there, I edited GPI (gene) a bit, but since there is no bot control template on the page any more, I wasn't sure if these changes will remain. I added the template myself manually, which I hope is what you need to do. However, finding and adding a template is probably beyond the capabilities of newbies, so although the new arrangement is cleaner, I think we still need to include this control template by default. Tim Vickers ( talk) 16:13, 9 July 2008 (UTC)
Hadn't noticed it! If you change the hidden text to "To stop automatic updates of the summary text change the update_summary field to "no" in the Template:PBB_Controls at the bottom of the page ." that is a bit more explicit. Tim Vickers ( talk) 17:55, 9 July 2008 (UTC)
Then we'll need to add text telling people to remove everything apart from the PBB template at the top. We need to make this as newbie-proof and approachable as possible. Tim Vickers ( talk) 20:37, 9 July 2008 (UTC)
Hello,
You have included this picture inside Category:Copyright holder released public domain images. However, the introductory statement at the top of that category says : "Please include all evidence you have that creator desires the image to be public domain on the image description page". Do you have any such statement that might be included in the image's description page ? Teofilo talk 13:38, 8 July 2008 (UTC)
The Ortholog section of the genes I've looked at ( such as ITK_(gene) ) list coordinates on mm8 at http://genome.ucsc.edu but the default at ucsc is mm9 ( until you visit and switch to another build ). Adding the db parameter to the url would solve this, it's &db=mm8 in the ones I've checked. PTGS2 is another example, the differences betwixt mm8 and mm9 have shifted it out of the browser window on mm9 —Preceding unsigned comment added by 198.129.91.135 ( talk) 00:56, 9 July 2008 (UTC)
I was just editing the C3orf58 page. I wanted to indicate that it may be regulated by MEF2 as the paper states. I tried to create a link to MEF2 and there wasn't one. But I realized there was a link to Mef2. So I used that.
However, Mef2 may not be human--that's a Drosophila symbol, it appears. And that page has 4 genes on it that appear to be the human ones. But they aren't MEF2, they are MEF2A, MEF2B, MEF2C, and MEF2D.
Not sure how to handle that. —Preceding unsigned comment added by Mary Mangan ( talk • contribs) 20:19, 11 July 2008 (UTC)
Ooops, I made this edit thinking I had a solution, but clearly the issue is deeper than that (as discussed here). Gotta run now, but feel free to undo any of what I did... Cheers, AndrewGNF ( talk) 02:11, 12 July 2008 (UTC)
Hi! I've noticed that some images uploaded by this bot, like Image:PBB GE FREM2 gnf1h07842 at tn.png or Image:PBB_GE_FREM2_gnf1h07842_at_fs.png, are in PNG format. Besides that all these images should be better uploaded into the Wikimedia Commons to be shared among all the different Wikipedias (and put into an adequate category there), I'd like to raise your attention about the following policy: Use SVG over PNG (and [7]). The SVG format is much more appropriate for this kind of images, offering more flexibility, more image quality and space efficiency, and the MediaWiki software ensures compatibility with all browsers. Thanks! — surueña 08:20, 11 July 2008 (UTC)
Hello folks--I've been trying to make some edits learn the ropes, and there are a few things that I thought I would add to the discussion. Feel free to edit/move/disregard/whatever.
1. It would have helped me if there was a box on the gene pages that pointed to the project goals, guidelines, templates, situations for new genes, etc. I had to sift through a bunch of different documentation to try to figure out what to do. And ask questions on the our blog and in the talk pages. Maybe there is some central location/forum (like here?), but I don’t know where it is or how to locate that. I guess I’m asking for a contributors’ forum or something?
2. The new gene creator template is helpful, but what would really help me is to have a whole mock page to simply copy/paste that had the right sections: a discussion section (and some lorem ipsum text is fine), and then some mock references all formatted right, subsections, and the box creator. I kinda tried to do that with the Map4 page, but that didn’t work out very well.
3. I have to advocate for some training…ok, that’s my job probably…but I think there are some people out there who would contribute if you could create a community around it with some support and some carrots (still not sure what the carrots are yet). Retired scientists, stay at home parents with science training, hobbyists, family members with genetic issues, in addition to the practicing scientists and students. But there needs to be some outreach and wrangling there.
Mary Mangan ( talk) 17:37, 11 July 2008 (UTC)
New comment: Is the Gene Wiki project the same thing as the Wikipedia:WikiProject_Molecular_and_Cellular_Biology one, as the box on the Talk:MAP4 page shows now? I went over to MCB to understand that better, but it isn't clear to me if it is part of the same thing. —Preceding unsigned comment added by Mary Mangan ( talk • contribs) 17:58, 12 July 2008 (UTC)
PBB links to UCSC for mitochondrial (MT) genes is not happening. See ND6, COX2 and the location links. The display looks like you'll get something at UCSC, but you won't. Needs to be chrM. There's some other oddness about the M genes, but I can't quite figure out what that is yet. Mary Mangan ( talk) 00:10, 12 July 2008 (UTC)
Dear Sirs, may I ask you four questions:
Yours faithfully, Simplicius, Germany
It would be useful to provide editors an easy way to edit the PBB template page, for example to replace the protein struture graphic, add missing EC numbers, etc. This can be accomplished rather ineligantly using the following syntax:
This places a small hyperlink labeled "edit" above the PBB box in the article. This solution is not ideal since (1) the syntax is rather messy and detracts from the simplification of using PBB template and (2) the hyperlink is placed above rather than in the template. A much better solution would be to add this functionity directly in the template rather than as a parameter to the template. Boghog2 ( talk) 17:48, 24 July 2008 (UTC)
e.g. with the wikilinks in this edit: http://en.wikipedia.org/?title=MAGEA3&diff=227790302&oldid=224566405 be reverted when the summary is updated? Thanks, -- Rajah ( talk) 07:50, 25 July 2008 (UTC)
I am kind of wondering at the utility of the protein boxes. Here are some basic questions I have. I noticed that on the HLA-DQA1 and HLA-DQB1 page it showed (I changed the name) a picture of HLA-DQ and called it HLA-DQA1, the same was true for HLA-DQB1. On the HLA-DR page it has a HLA-DRA gene and a picture of an HLA-DR molecule. Also in error it claims there are no mouse homologs, the homolog for HLA-DQ in mice is MHC-IA, so that bit of information is also wrong. The repository for HLA sequence information is IMGT/EBI, not pubmed, so it is much better to have a protein box that uses IMGT/EBI as a source of information. The final issue is it displays a list of images but some of these images are minor variations used as a part of single studies. Even for someone who has created pages on all the HLA-A and HLA-B, I think that so much information is a waste, its like having a full author list when author1, author2, author3, et al. will do. In addition the box contains three graphs with essentially the same information whereas it has been known since 1970 and is listed in the DR, DQ and DP pages that these antigens are found on lymphoid tissues. The protein box extract placed as the lead paragraph is not wikified and cannot be wikified. I can go on. What is the benefit of doing this if it simply throws trivia onto pages? Also if a person finds an error in the box and corrects it, the next update will override the correction, probably with the same incorrect information. That process overrides expert review of materials. PB666 yap 05:21, 27 July 2008 (UTC)
Thanks guys for sorting this all out. The pages look great. I gotta admit, I'm a bit glad I was late to this party. Longstanding confusion from my days as an undergrad leaves antigen presentation (and adapative immunity, in general) as one of my carefully nurtured areas of ignorance. ;) AndrewGNF ( talk) 17:23, 28 July 2008 (UTC)
Thank you for uploading Image:PBB Protein NFAT5 image.jpg. However, it currently is missing information on its copyright status. Wikipedia takes copyright very seriously. It may be deleted soon, unless we can determine the license and the source of the image. If you know this information, then you can add a copyright tag to the image description page.
If you have uploaded other files, consider checking that you have specified their license and tagged them, too. You can find a list of files you have uploaded by following this link.
If you have any questions, please feel free to ask them at the media copyright questions page. Thanks again for your cooperation. Sdrtirs ( talk) 16:13, 14 August 2008 (UTC)
Thank you for uploading Image:PBB GE TLK2 212986 s at fs.png. However, it currently is missing information on its copyright status. Wikipedia takes copyright very seriously. It may be deleted soon, unless we can determine the license and the source of the image. If you know this information, then you can add a copyright tag to the image description page.
If you have uploaded other files, consider checking that you have specified their license and tagged them, too. You can find a list of files you have uploaded by following this link.
If you have any questions, please feel free to ask them at the media copyright questions page. Thanks again for your cooperation. Sdrtirs ( talk) 16:15, 14 August 2008 (UTC)
Hi! Could I copy the contents of the protein box, for example, from the NOTCH1 when I create a page in the Russian Wiki? If yes, how do I do this? Thanx. -- CopperKettle ( talk) 04:37, 19 August 2008 (UTC)
Your bot has uploaded hundreds of duplicate images. One example:
Was this intentional? And if so, what can we do to eliminate these duplicates? Image redirects now work. So perhaps for a case like this, the image could be re-uploaded as Image:PBB_Protein_PUM_image.jpg and then delete the files at PUM1 and PUM2 and make them redirects? Let me know your thoughts. One thing that's clear is that having all of these duplicates is not a good situation. -- MZMcBride ( talk) 02:28, 15 September 2008 (UTC)
Obviously there is a difference between proteins and genes. Why are there hundreds of pages (e.g. GPR3) that incorrectly state that so-and-so protein is a "human gene"? Perhaps the protein and the gene that codes for it have similar names, but that is no reason to conflate the two. It would be absurd to go through and correct all the articles with this error. Perhaps a bot could do it? Fuzzform ( talk) 00:03, 2 October 2008 (UTC)
Sorry, traveling this week, but will reply as soon as I get a chance... Just didn't want anyone to think they were being ignored (especially when they come offering to participate!) AndrewGNF ( talk) 06:44, 9 October 2008 (UTC)
Hello AndrewGNF. Thank you for uploading the Gene expression pattern diagrams. I would like to ask you for uploading the images in future on Wikimedia Commons. Then other Wikis are able to use the images, too. Thanks a lot! Regards, -- Bcr-abl ( talk) 10:22, 7 October 2008 (UTC)
Hi Andrew, is there any way the bot could check for alternate names for a gene/protein before it goes ahead and creates an article? I've been trying to link up all the tyrosine kinase articles. I keep coming across articles that have been created by the bot, were an article already exists under the proteins alternate name, see NTRK3 and TrkC, I'll leave these as they are for now as an example. K.murphy ( talk) 13:54, 10 November 2008 (UTC)
If a protein summary contains a technical term that should be linked to its Wikipedia article but isn't, what is the correct way to proceed? Please document this at the relevant template pages. Thanks, AxelBoldt ( talk) 00:39, 31 December 2008 (UTC)
I am trying to built up a portal using two templates to make it a bit easier. The elements of each page can be changed quite easily. What elements are needed? Please feel free to do changes and to fill the elements with contents. Simplicius ( talk) 16:57, 30 July 2008 (UTC)
I think we absolutely want to maintain and emphasize our connection with WP:MCB. How should we do this? In my mind, this portal will serve two purposes. First (and most obviously), an organizational hub for people who want to focus on gene and protein annotation. Second, I hope many people come to edit the gene wiki through past and upcoming press -- and these newbies will be true novices. I hope this portal is a gentle landing point for those people... AndrewGNF ( talk) 01:10, 1 August 2008 (UTC)
The portal uses two templates to generate new paragraphs:
Thx! Simplicius ( talk) 12:48, 6 August 2008 (UTC)
Andrew, (no critics, just a question) why do you prefer an [edit]-function via web address instead of wiki link? Simplicius ( talk) 13:41, 6 August 2008 (UTC)
Please use this template for some "advertisment".
About the portal, please develope the primal questions for interested users:
You started already. Please go on.
And please try to put the works' output (WP articles etc.) onto the first page portal as an entertaining and informing page, and the technical hints and helps onto the second page Gene Wiki – Facilities. Simplicius ( talk) 14:00, 6 August 2008 (UTC)
I will try to find the tools for supervising articles in a category so that you can see changes automatically. Please allow me a question: is there are certain category for articles generated by this project or by your tools? -- Simplicius ( talk) 13:41, 6 August 2008 (UTC)
Link - very cool. Tim Vickers ( talk) 02:19, 4 September 2008 (UTC)
I know there is an article now, which is great, but what happened to the nice description and images like these: Image:PBB_flowchart.png, Image:PBB_flowchart_Sub.png? It would be really great to have an updated, detailed article. -- Dan| (talk) 14:07, 4 November 2008 (UTC)
I found this page via "PLoS Biology - Metagenome Annotation Using a Distributed Grid of Undergraduate Students".. After half an hour I still have no idea from this page how I may begin to annotate. Is this not a lack in a basic purpose of the page? Mccready ( talk) 01:36, 26 November 2008 (UTC)
Dear Mr. or Ms. Bot: The double-column format for Further Reading does not look so good on my computer. The single-column format at ST3GAL3 looks much better. Can you fix yourself so you output the Further Readings in single column? Sincerely, your friend, GeorgeLouis ( talk) 05:08, 30 April 2009 (UTC)
Yes, it looks very nice. GeorgeLouis ( talk) 17:55, 30 April 2009 (UTC)
Does anyone happen to remember where our last discussion of the lead sentence of PBB articles is? The best I can find is in User_talk:ProteinBoxBot/Archive2#Protein_vs._Gene, but somehow I seem to remember a more detailed discussion with several options. Hoping someone else's memory is better than mine... Cheers, AndrewGNF ( talk) 18:09, 30 April 2009 (UTC)
Is is possible for PBB to include wikilinks in the summaries it provides using the PBB_Summary tempalte? For example, TNFRSF21 would benefit from several wikilinks. Most articles in PBB's scope probably have similar stub-like articles, with a brief lead having one or two wikilinks to general terms, and then a paragraph from PBB that has some specific terms that are obscure to a typical reader. In the TNFRSF21, for example, NF-kappaB, MAPK8/ JNK, TRADD are meaningless to almost everyone outside of molecular biology. And the following terms are probably meaningless to most people outside of general biology: TNF-receptor, apoptosis, domain, receptor, signal transduction, knockout, T-helper cell.
I suppose it might be difficult to have PBB identify which terms should be linked, whether that term has a corresponding Wikipedia article, and whether the article matching that term is actually about the intended topic (a link to " knockout", for example, would lead to something other than knockout gene). — Twas Now ( talk • contribs • e-mail ) 10:22, 24 May 2009 (UTC)
[[TRADD]]
; when it comes across "JNK", it will change it to [[c-Jun N-terminal kinases|JNK]]
. Ambiguous terms should generally not be added to the whitelist. For example, if PBB comes across "knockout" but not "knockout gene", there is a slight (...very slight) chance it might mean a literal
knockout, and not
knockout gene. There are more plausible examples, with subtler ambiguity, but I already used this one above... in reality, it would probably be fine to link
knockout gene in all cases. —
Twas Now (
talk •
contribs •
e-mail )
18:04, 24 May 2009 (UTC)Anyone watching here might be interested in this topic: Wikipedia_talk:WikiProject_Molecular_and_Cellular_Biology#Relating_gene_pages_by_protein_interactions. Cheers, AndrewGNF ( talk) 22:47, 25 June 2009 (UTC)
For anyone concerned Protein Box Bot will be making some page edits soon. See the announcement here. JonSDSUGrad ( talk) 00:21, 23 July 2009 (UTC)
Two more that I found and reverted, just for the record... [16] and [17] AndrewGNF ( talk) 03:00, 28 July 2009 (UTC)
A request for comment has been made at the above link. Your input is welcome. Boghog2 ( talk) 20:32, 19 August 2009 (UTC)
We've created the version 0.1 tool for generating a Gene Wiki page on demand, modeled after Diberri's template filler. It's hooked up to our BioGPS application, accessible at http://biogps.gnf.org. So that the default output is focused on the GeneWikiGenerator tool, most users here will be interested in using this URL: http://biogps.gnf.org/GeneWikiGenerator/. From there, search for your favorite gene by most public identifiers, symbols or aliases (or try one of the example queries), and then select one of the returned genes in the left-hand "Current gene list". You'll then see two windows. The bottom one has the Wikipedia page for the gene, if one exists. The top one has the wikitext and instructions for creating or updating a gene page according to the standard "Gene Wiki" format. If people here have a chance to try it out, we'd love to hear feedback.
(As a plug for BioGPS more generally, you can see the other gene report views by changing the "current layout" in the upper right. If you register for a free user account, you can further customize your layouts by mixing and matching any of the 150+ plugins in the plugin library. Any comments on BioGPS in general are also welcome... </shameless_plug>) Cheers, AndrewGNF ( talk) 00:11, 27 August 2009 (UTC)
Hi Tim. Thank for all your excellent work. Did somebody go through all the human gene locations and edit out the locations? It seems as though they used to list gene location using the old cytogenetic band tags (like "15p2.23") Next they seemed to change to a numeric address expressed in megabasepairs (which I suppose they needed to abandon because there is so much intervariability in humans....like the variable region of triplet repeats that result in fragile- X syndrome). But "n/a" is not useful. At least the old cytogenetic terminology could get you in the ball park. Last year I built a large map that labels the cytogenetic bands, and there is an approximate scale so that users could at least get close to locating what they were looking for. If we're ever going to understand the architecture of the genome, we'll need to create tools to help us see the relationships (Entrez Gene is OK, but it's so "all-inclusive" that it's hard to find anything.) Tim, I'd like to help, but I'm not sure where to start. doctorwolfie ( talk) 14:16, 4 September 2009 (UTC)
I'm looking for some examples of edits to gene pages and I'm hoping people watching here might have suggestions. I want to highlight one (or ideally a handful) of edits that satisfy these two criteria: 1) includes a citation to a scientific reference, and 2) adds information that could be expressed as a Gene Ontology annotation but hasn't been done so by the annotation authorities. For example:
Hmmm, I guess not terribly hard to find, but perhaps people here have particularly good examples to highlight? Cheers, AndrewGNF ( talk) 01:32, 9 September 2009 (UTC)
I am an author of the German wikipedia and also edit sometimes in the English wikipedia, mainly on biochemistry articles. I have been active on some gene articles and I noticed that the GNF Protein box and the GNF Ortholog box templates have a lot of useful links to other databases but these mainly cover single genes or gene products (like Entrez, Ensembl and Uniprot) but a link to a phylogenetic database is not present. So I felt that there would be a lot of added value if there were a direct link to a phylogenetic database that lists orthologs of a specific gene. This would allow the exploration of its corresponding genes in hundreds of complete genomes. There are already links from Uniprot to phylogenetic databases but you have to scroll all the way down to find them.
I am currently working with a group at ETH that created the OMA-database ( http://www.omabrowser.org). It is one of the biggest orthology databases and many other website such as Uniprot and Ensembl link to OMA. Since I know this project best I would suggest to integrate this website into the GNF Protein box but there are also other projects which might be more suited for Wikipedia. On the technical side, the change in the infobox would only consist of a small adjustment since the database could be called directly with the uniprot entry ID (e.g. http://www.omabrowser.com/cgi-bin/gateway.pl?f=DisplayEntry&p1=PROCA02187 in the case of OMA). Did you discuss such an idea already? What do you think? Greetings -- hroest 12:07, 9 September 2009 (UTC)
As discussed previously, there is a consensus to change the lead sentence to make clear that Gene Wiki pages are about both the gene and the protein encoded by that gene. The consensus reached was that the opening sentence (using GPR3 as an example) should read as follows:
Perhaps this should be modified slightly according to this as follows (replacing "which" with "that" is probably a good idea although the additional two commas in my opinion is over doing it):
In addition, the name should probably be taken from the UniProt database (protein name) rather than HUGO (gene name) while the gene symbol would be as before (i.e., the HUGO gene symbol). The UniProt protein name is often the same as the HUGO name, but sometimes differ (compare for example estrogen receptor beta where the UniProt name is "estrogen receptor beta" while the HUGO name is "estrogen receptor 2 (ER beta)".
Given the never ending controversy that this opening sentence has generated, I would like BogBot to get started on this in near future. I think it will be straight forward to write a regular expression that will recognize and replace the existing boiler plate lead sentence and leave untouched any sentence that a human editor has modified.
Thoughts concerning the two minor changes proposed above? Also how best to proceed (bring this up again with the MCB project followed by WP:Bots/Requests for approval)?. Cheers. Boghog ( talk) 13:53, 27 September 2009 (UTC)
Following a discussion here, I've written a draft program which takes in a PDB ID and outputs a ray traced image of the corresponding structure. When I enter standard commands to make the image's background transparent in PyMOL (using version 0.99r6 on Windows), however, I can't seem to make them work. Specifically, entering 'set ray_opaque_background, 0' and/or 'set opaque_background, 0' does not result in the expected checkerboard background indicating a transparent background (see a relevant entry in PyMOLWiki here: http://pymolwiki.org/index.php/Ray_opaque_background). Using the GUI to select 'Display' -> 'Background' and uncheck 'Opaque' and then check 'Show Alpha Checkerboard' does nothing. This is odd, because I've made backgrounds transparent in PyMOL before (see [25], [26]). Has anybody run into a similar problem? Trouble-shooting via Google hasn't helped. Emw2012 ( talk) 14:10, 27 September 2009 (UTC)
(unindent) I think I may have found a workaround to the cropping issue by using GIMP -- simply autocrop the image and add some fixed number of pixels (e.g., 25) as padding. Presumably this will be the solution once I find out how to incorporate the simple process for the fix into a batch script. However, while the image itself looks good, it seems to be deformed once its added to the 'GNF Protein box' template. The problem is viewable at User:Emw/PDBImageTestcases_2. Any ideas on what may be causing this? Emw ( talk) 00:51, 15 November 2009 (UTC)
Has the SCOP classification feature of the 'Automate PDB uploads' project proposal been implemented ( Portal:Gene_Wiki/Project_proposals#Automate_uploads_of_PDB_images)? The automation needed to implement the SCOP feature seems straightforward in concept: go to the SCOP website, enter the PDB ID of interest into the search form, and parse from the retrieved lineage any elements of interest.
Which elements of a SCOP lineage should be retrieved by the feature (e.g., class, fold, superfamily, family, protein, and/or species)? And where should the information on the elements be put -- somewhere as a new field in one of the templates used by ProteinBoxBot, and/or in a newly added 'Summary' box in the image file itself (e.g. File:PBB_Protein_MMP9_image.jpg)? Emw ( talk) 16:12, 4 November 2009 (UTC)
Typically, gene articles containing protein structure images are titled in the form <HUGO symbol> (e.g. MMP9) or <HUGO symbol>_(gene) (e.g. PIR (gene)). Of the 2774 articles having structure images, there are about 221 that don't follow either of those two naming conventions. For example, consider interleukin 6, with the HUGO gene symbol IL6 -- IL6 is a disambiguation page and IL6 (gene) doesn't currently exist. Would it make sense to add IL6 (gene) as a redirect for this article, and to apply this pattern to the roughly 10% of gene articles with structure images that are not accessible via HUGO gene symbol? Emw ( talk) 21:31, 24 December 2009 (UTC)
Hi folks, I'm looking at merging all the different Telomerase RNA component articles that WP has amassed. At the top of the page is an odd phrase 'n/a (protein)n/a (protein)'. I suspect this is coming from the 'PBB|geneid=7012' template. I guess something in the template is spitting the dummy because this is not actually a protein. Is there a quick fix?-- Paul ( talk) 08:09, 9 October 2009 (UTC)
Is integrin α4β7 (called LPAM-1, lymphocyte Peyer's patch adhesion molecule 1, here) the same as ITGB7? And while I am at it: Alpha-v beta-3 is probably the same as a ProteinBoxBot-created article, but which? -- ἀνυπόδητος ( talk) 11:04, 14 October 2009 (UTC)
According to WHO, glycoprotein 72 is the target of several monoclonal antibodies ( anatumomab mafenatox, minretumomab, indium (111In) satumomab pendetide). It seems to be the same as CA 72-4, but I'd like to be sure before I create a redirect. Can anybody help? -- ἀνυπόδητος ( talk) 18:50, 24 October 2009 (UTC)
The image is actually of HuC (ELAVL-3), not HuD (ELAVL-4). Only two structures exist in the PDB, both RNA-bound dimers. These are 1FXL and 1G2E. regards, Sunil060902 ( talk) 17:17, 27 October 2009 (UTC)
The Bot that does the protein images added the full chemical name of titin, a ridiculous amount of characters, could this be fixed? -- The New Mikemoral ♪♫ 06:12, 16 November 2009 (UTC)
BogBot changed the bolded name of this protein so it doesn't match the article title any more. It should be merged with EpCAM anyway, but in which direction? And how is this done without breaking the {{ PBB Summary}}? -- ἀνυπόδητος ( talk) 12:36, 16 November 2009 (UTC)