Wikipedia talk:WikiProject Molecular Biology/Gene Wiki/Archive 2

message: 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)
replies: text: For the record, i found this discussion. David D. (Talk) 06:03, 5 February 2008 (UTC)
replies: text: Yeah, I think this is one of those cases where a given term refers to both a specific gene/protein as well as a protein family.  Not sure what the best solution is here...  AndrewGNF (talk) 06:07, 5 February 2008 (UTC)
replies: text: May be there is no solution, but the two boxes don't work from an aesthetic perspective. One possibility might be to add some new fields for family identifiers into the PBB template that could then be used in these rarer cases. At least then there would be only one box.  Have you been in contact with , he seems to have been the one to code this box? David D. (Talk) 06:17, 5 February 2008 (UTC)
replies: text:  I think adding PFAM as optional fields to the PBB template as already suggested in the PBB version 2 specs (import and display protein domain information (through Uniprot/PFAM/COGs)) would solve the problem. Boghog2 (talk) 07:08, 5 February 2008 (UTC)
replies: text: OK, thanks, I didn't check there, it will make a lot more sense than having two boxes. David D. (Talk) 07:09, 5 February 2008 (UTC)

text: Should be pretty straightforward to add new optional fields to the PBB templates.  Obviously they won't get populated by PBB until V2, but that will at least allow merging of the boxes when they appear on the same page.  But, I'm still not completely sure they should be merged.  Check out what Special:Whatlinkshere/Template:Pfam_box.  These are clearly protein families, not individual protein/genes.  I almost think that we should split Catalase into two articles -- one on properties of the protein family, and one on specific functions of the catalase gene which happens to share that same name. AndrewGNF (talk) 16:50, 5 February 2008 (UTC)
replies: text: And just to clarify, the V2 addition will be to add pfam links -- one gene to many PFAMs.  So that seems to be a slightly different goal than the Pfam_box, which is meant to give information about one and only one PFAM entry.  AndrewGNF (talk) 16:54, 5 February 2008 (UTC)

text: Of course it would be a great improvement to include Pfam and possibly InterPro links in Protein Box, as was discussed previously. Just remember: this requires to use domain structure of the protein. Different domains of the same protein may belong to different Pfam families. Simply making a Pfam link for each domain of the protein would resolve this (if there are several identical domains in the protein, onle link might be enough). The Catalase is a perfect example of inappropriate merging of an article about a specific human     protein, and an article about protein family/domain. Such articles must always remain separate but refer to each other.Biophys (talk) 18:29, 5 February 2008 (UTC)
replies: text:  This may be a semantic question, but I consider the subject of the catalase article to be about the enzyme of which the human variant is one example. In my opinion, information about the human enzyme is therefore appropriate to include in the article.  It is also important to point out that in its present form, the PBB template already contains information on more than just the human protein/gene, in particular the EC number and HomoloGene links.   While splitting articles into protein families and the specific human protein is a possibility, I would argue that this may unnecessarily fragment closely related information, especially considering the majority of these articles are presently stubs.  In the case of catalase, there is probably enough material  to split the article. So if someone went ahead and split the catalase article, I wouldn't object.  Boghog2 (talk) 19:58, 5 February 2008 (UTC)
replies: text: I agree, there are multiple right answers, and each example is probably a judgment call of the person dealing with the page.  AndrewGNF (talk) 20:09, 5 February 2008 (UTC)
replies: text: The Boghog2 suggestion is valid (I agree) when there is only one human protein from the family, i.e. only one human catalase. If there were several human catalases, one could include them all in one article, but I would recommend to avoid this.Biophys (talk) 20:51, 5 February 2008 (UTC)
thread_title:  more identifiers 

message: 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)
replies: text: That's pretty exciting.  It just shows how wikipedia can be used by scientists to get this information out there.  It's not about how good the information is, we all know there are excellent science web sites out there. Most important is where the information is hosted, in this case wikipedia. David D. (Talk) 18:51, 6 February 2008 (UTC)
replies: text: And if I may articulate David's thought one step further...  With all the great science web sites out there, it's pretty much only one-way transfer of information.  If web users see incomplete/inaccurate information, their only recourse is to yell and curse at the screen.  Here at WP, of course, they can fix the error or omission.  This is really the first two-way gene portal, qualitatively different than the rest.  (I know, I know, I'm preaching to the choir here...)  AndrewGNF (talk) 19:24, 6 February 2008 (UTC)
replies: text:  Congrats Andrew and Jon!  I agree that this is a very impressive result.  The WP pages seeded by PBB are a great start which I hope will attract more experts to flesh out the details.  Already they represent a convenient first stop of useful links to other sources of information.  Furthermore the PBB expression data is unique in its accessibility and breadth.  Bravo Brava Bravi!   Boghog2 (talk) 19:46, 6 February 2008 (UTC)
thread_title:  google ranks 

message: 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)
replies: text: Hello, thanks for the note.  This is actually the exact issue that was discussed (and recently resolved for one image) in the section above.  We'll work on now making that change for all images that were previously uploaded.  AndrewGNF (talk) 16:56, 8 February 2008 (UTC)
replies: text: Cool, thanks!  And sorry I missed the last section! -- Lea (talk) 21:49, 8 February 2008 (UTC)
thread_title:  Sources 

message: 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)
replies: text: The tumor necrosis factor receptor article is about a fairly large protein family so a Pfam box on this page would be appropriate.  Individual articles about many of the family members with PBB content already existed but not all were linked from the parent article. Finally there were a few family member pages without PBB content.  The Pfam box, missing links and PBB content have now all been added.  Cheers.  Boghog2 (talk) 12:07, 9 February 2008 (UTC)
thread_title:  We need genes here 

message: 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.  
:Online and printed resources are welcome to include 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, and their corresponding citations are included.
Breaking it down plainly:
*Attribution is required in all instances.
*Commercial use of the images is allowed if the images are part of a publication.
*Commercial use is prohibited if you wish to sell the images individually.
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)
replies: text: Tim, can you take the lead and follow up with the person you've been emailing at the PDB for clarification?  (I'm happy to do it as well if you send me contact info...)  Thanks... AndrewGNF (talk) 17:44, 6 February 2008 (UTC)

text: I think the final decision on this was that we need to use the  tag rather than . Tim Vickers (talk) 17:34, 10 February 2008 (UTC)
thread_title:  Simply ''not'' Public Domain 

message: 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  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  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)
replies: text: Why does everyone always pick on the image for the NIPA1 gene?  ;)  Nv8200p, thanks for the note.  Do you have a suggestion on how to appropriately tag it?  The images were created by me.  We originally tagged it with , but MZMcBride pointed out that this tag is probably not appropriate for a bot-uploaded image.  (See User_talk:ProteinBoxBot/Archives/Archive1#ProteinBoxBot.27s_uploads.)  We then switched to , where the attribution goes to my employer.  If we need to specify any further "source", please suggest how we should do this.  Thanks, AndrewGNF (talk) 00:13, 8 February 2008 (UTC)
replies: text: Is there any publication where the data from which the graph was created was printed, preferably a peer reviewed journal or reliable magazine, but a company produced article would work. If this data has not been published then the graph might be considered original research. -Thanks Nv8200p talk 01:37, 8 February 2008 (UTC)
replies: text: The data come from this article: .  Should the article itself then be listed as the source? AndrewGNF (talk) 02:21, 8 February 2008 (UTC)
replies: text: Yes. I set up it up on the image description page. Please edit it and make it right as I was just guessing at the description. -Regards Nv8200p talk 03:52, 8 February 2008 (UTC)
replies: text: Super, thanks much...  AndrewGNF (talk) 05:56, 8 February 2008 (UTC)

text: ;) I don't envy your job (if one can call it a "job"...)  AndrewGNF (talk) 06:07, 8 February 2008 (UTC)
replies: text: I do not think this is really a "job". This is more like entertainment. Consder this La Comédie humaine where you are one of actors. Biophys (talk) 03:32, 10 February 2008 (UTC)
thread_title:  Unspecified source for [[:Image:PBB_GE_NIPA1_gnf1h07157_at_fs.png]] 

message: Hi, please have a look at ; 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)
replies: text: Hi, the problem (I think) is not with the ProteinBoxBot, but the tool used to create the citation.  As explained here, some URLs and DOIs contain special characters which cause the wiki link to break.  Fortunately there is an easy fix: replace the special characters with their hexidecimal equivalents as I have done here to the Luo et.al citation.  User:Diberri graciously fixed the problem with the URLs, but apparently not with the DOIs.  I will ask have asked him to fix the DOIs as well.  Cheers.  Boghog2 (talk) 22:23, 10 February 2008 (UTC)
thread_title:  doi weirdness 

message: 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,  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)
replies: text: For whatever it's worth to you, see . Stephen Ewen (talk) 06:52, 13 February 2008 (UTC)
replies: text: Thanks Stephen...  For simplicity, let's take all the follow-up to Wikipedia:Media_copyright_questions#Protein_Data_Bank where hopefully we can get some clarity on a game plan... Cheers, AndrewGNF (talk) 18:24, 13 February 2008 (UTC)
thread_title:  Not {{Tl|Attribution}}, either 

message: 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)
replies: text: (I moved Tim's comment from User:ProteinBoxBot/Google_Summer_of_Code_2008 for discussion here.)  So just to be sure I understand...  We'll adjust PBB so that EC number is properly noted in the infobox and links to the corresponding enzyme page (through a redirect of the EC number).  Creation of enzyme pages is in progress (done?) by Daisy, and those will be linked back to the human gene page.  Sound right?  If so, then PBB (or some offshoot) will only be responsible for getting ECs to show up correctly in human gene pages? AndrewGNF (talk) 23:06, 4 March 2008 (UTC)
thread_title:  Integration between enzyme and gene pages 

message: 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  and . Melchoir (talk) 09:25, 6 March 2008 (UTC)
replies: text: Thanks, fixing this issue for newly-created pages is definitely on our to do list.  Cheers, AndrewGNF (talk) 00:54, 17 March 2008 (UTC)
replies: text: Okay, great! Melchoir (talk) 17:37, 19 March 2008 (UTC)
thread_title:  Newline layout issue in created articles 

message: 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)
replies: text: Personally, I think the current behavior (linking to geneontology.org) is the best option.  I think linking to WP pages would only be good if it were done in concert with a GO term stub creation effort, and even then I'm not sure it's the best option.  (For example, what additional info would you add to those pages, besides the ontology term and a link to a central resource?)  Having said all that, technically speaking it would be an easy change and we'll gladly comply with the community consensus.  If you'd like to pursue this further, I'd suggest taking it over to Wikipedia:WikiProject_Molecular_and_Cellular_Biology/Proposals for more discussion.  Cheers, AndrewGNF (talk) 01:00, 17 March 2008 (UTC)
thread_title:  GO terms - internal links 

message: 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)
replies: text: This is an issue that we noticed before and I think we fixed it for future pages.  Essentially PBB was uploading the images fine but not adding the appropriate wiki text.  Anyway, I don't think the problem is too widespread, and the naming convention is pretty easy to add manually (e.g., ).  (The image is always taken from the first PDB entry listed.)  If you notice more than a handful of these cases, please let us know and we'll investigate further...  AndrewGNF (talk) 01:07, 17 March 2008 (UTC)
thread_title:  Protein pictures 

message: 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)
replies: text: Fixed!  Thanks... AndrewGNF (talk) 22:18, 2 April 2008 (UTC)
thread_title:  Image copyright problem with Image:PBB GE PPP4R1 201594 s at tn.png 

message: 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)
replies: text: Fixed!  Thanks... AndrewGNF (talk) 22:17, 2 April 2008 (UTC)
thread_title:  Image copyright problem with Image:PBB GE DMTF1 203301 s at tn.png 

message: There is a fault with SLC47A2 -wrong name at the beginning   ♦Blofeld of SPECTRE♦      $1,000,000?  17:32, 9 April 2008 (UTC)
replies: text: Good catch.  I've fixed it by hand for now.  This error was due to the recent changes by NCBI (note the 29-March-2008 last-edit date) and the subsequent stale data in our database.  Definitely hope to reduce this window in the future...  Thanks for the note.  Cheers, AndrewGNF (talk) 17:42, 9 April 2008 (UTC)
thread_title:  Fault 

message: Hey, could the maker of this bot be so kind as to include 
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)
replies: text: Yup, it's on the list of things to do.  (Both adding the template to new pages and adding it to previously-created pages...)  Cheers, AndrewGNF (talk) 00:52, 14 April 2008 (UTC)
replies: text: I went ahead and added the template to all new pages made by ProteinBoxBot after January. January & before are still lacking the template. I won't worry about it if it's on your to-do list, seeing how many pages there are just of articles made in January. ;-) Nagelfar (talk) 02:54, 14 April 2008 (UTC)
replies: text: Well, if you're doing it in some sort of automated manner, we'd certainly welcome the help doing all of the retroactive changes (leaving us to focus on the new pages).  If not, no worries, we'll get around to it.  cheers, AndrewGNF (talk) 02:59, 14 April 2008 (UTC)
thread_title:  MCB template in discussion pages? 

message: 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)
replies: text: Upon further inspection, I think I was wrong. Please disregard everything I ever said or did. ----Seans Potato Business 16:28, 20 April 2008 (UTC)
replies: text:  (well, I don't know if I'd go that far... Anyway, had the response all typed out, and I guess that others may have the same question.)  Hi there.  Yes, it was a conscious choice to default the page name to the gene symbol instead of the gene description (I know there's a discussion in the archives here of the village pump discussion...)  In many cases, the gene description is quite convoluted.  For example, do we really want ABCB7 to be moved to ATP-binding cassette, sub-family B (MDR/TAP), member 7?  ATP6V1B1 or ATPase, H+ transporting, lysosomal 56/58kDa, V1 subunit B1 (Renal tubular acidosis with deafness)?  CBFA2T3 or Core-binding factor, runt domain, alpha subunit 2; translocated to, 3?  Anyway, lots of really gross examples like this.  Having said that, I'm open to changing the behavior if there's consensus to.  AndrewGNF (talk) 16:44, 20 April 2008 (UTC)
replies: text: I wonder if the bot could automatically create redirects from the alternative names, though? ----Seans Potato Business 10:34, 21 April 2008 (UTC)
replies: text: Yeah, in theory it could but is there much value in putting a redirect from a horribly obscure gene/protein name?  In my ideal world, the article would be at the most common gene/protein name, to which the symbol would redirect.  Unfortunately I think that requires some amount of human intervention, so thus far we've just relied on knowledgeable editors stumbling on the page.  But we're certainly open to revisiting this if we can come up with some hard and fast rules... AndrewGNF (talk) 04:14, 22 April 2008 (UTC)
thread_title:  Incorrect naming of articles 

message: 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  command. 
I'm adding this same comment on the Template:PBB Control talk page. ~ Jotomicron 15:53, 23 April 2008 (UTC)
replies: text: Thanks for the feedback.  Yes, this is a known issue, and we hope to the problem fixed soon for both previously created pages and future pages.  Cheers, AndrewGNF (talk) 17:35, 23 April 2008 (UTC)
thread_title:  Empty line 

message: 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)
replies: text: Taken care of...  Thanks Fvasconcellos!  AndrewGNF (talk) 22:04, 24 April 2008 (UTC)
thread_title:  Image copyright problem with [[:Image:PBB Protein PPARA image.jpg]] 

message: * A ProteinBoxBot link to "Bioinformatic Harvester" would be nice
(http://harvester.fzk.de)
* Example directly via IPI: http://harvester.fzk.de/harvester/human/IPI00218/IPI00218982.htm
* Example via query: http://harvester.fzk.de/cgi-bin/human/search.cgi?zoom_query=brca1
..a very nice bot by the way...thanks :-) Ivo (talk) 05:39, 15 May 2008 (UTC)
replies: text: Thanks for the note.  I've added it to our ideas page.  Though adding additional links will likely require consensus from the community.  Cheers, AndrewGNF (talk) 17:09, 25 June 2008 (UTC)
thread_title:  Bioinformatic Harvester 

message: 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)
replies: text: Thanks, I've added it to the ideas page -- something I'm sure we can get implemented before any future mass runs...  Cheers, AndrewGNF (talk) 17:09, 25 June 2008 (UTC)
thread_title:  Endash 

message: 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  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  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)
thread_title:  Speedy deletion of [[:Image:PBB GE PCDHB11 221408 x at tn.png]] 

message: 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)
replies: text: Thanks for the note.  Believe it or not, this current round of edits is actually removing a lot more of those empty paragraph lines than it's creating (e.g., SIM2, STIL, SGSH, randomly chosen from recent edits).  Providing examples like the one above will definitely help us improve our parsing mechanism though, so feel free to let us know if you notice any others.  Thanks, AndrewGNF (talk) 13:31, 9 July 2008 (UTC)
thread_title:  bot is creating unnecessary empty paragraph 

message: 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)
replies: text: Hi, thanks for the note.  Sorry to swamp your small crew.  Is there way for you to exclude bot edits, or edits from a given user account?  I'd normally be happy to dial it back a bit, but we're in a bit of a rush.  We've just published an article that's getting a fair bit of press, and we're hopeful that this will attract a large number of newbie scientists to edit gene pages.  Our rush comes from the realization that pages like this can be pretty intimidating for a newbie to wade through, but this change makes things much more friendly.  Anyway, if you can tolerate a swamped list for just a bit longer (I think we're almost done), I think it would really be a net win for WP.  thoughts? AndrewGNF (talk) 18:04, 9 July 2008 (UTC)
replies: text:  Well, if it's only going to be like this for another day or so it's probably ok - I was just worried this might become a regular thing. And I understand if you think there may be a flood of new recruits. Grutness...wha? 01:51, 10 July 2008 (UTC)
replies: text: Nope, it won't be a regular thing.  Last I checked the edits should be finished today.  Thanks for bearing with us...  Cheers, AndrewGNF (talk) 12:18, 10 July 2008 (UTC)
thread_title:  A request from a new template patroller 

message: 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)
replies: text: Hi Tim,  The latest PBB run actually moves the control template to the bottom of the page.  Do you think that's too hidden for people to find?  I edited GPI (gene) to reflect that (copied your new template over the old one at the bottom), but on second thought I probably should have asked your input on whether this is clear enough beforehand.  Thoughts?  In practice though, we're going to put a lot of thought into things before we do an update run though.  I'm even contemplating removing the PBB_Summary template completely.  My guess is that the summary doesn't change very much, and I think it's confusing for people who are editing the text.  Plus, as I've said before, once the summary gets touched at all by a human editor, I think PBB should not overwrite that text ever.  Anyway, discussion on all these issues are welcome... AndrewGNF (talk) 16:35, 9 July 2008 (UTC)

text: Ahh, I've actually just removed that comment completely.  If PBB doesn't find the PBB_Summary template, it won't try to re-add it in or anything, even if the PBB_Controls has update_summary=yes.  You think that works okay?  AndrewGNF (talk) 18:08, 9 July 2008 (UTC)

text: Sorry, not sure what you mean here.  Are we talking about GPI (gene) in particular, or the PBB gene pages in general?  AndrewGNF (talk) 12:19, 10 July 2008 (UTC)
replies: text: Gene pages in general. Otherwise there is the risk of people not removing the template because they don't want to "break" anything. Tim Vickers (talk) 14:40, 10 July 2008 (UTC)
thread_title:  Bot control template 

message: 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)
replies: text: Sorry, not exactly sure what you think should be added.  We have a link there to the pdb, and the pdb releases their data into the public domain.  do you suggest we replace the generic www.pdb.org link to the specific license page (which I can't find at the moment, but was referenced ad nauseum in some previous discussions on pdb licensing)?  AndrewGNF (talk) 13:41, 9 July 2008 (UTC)
replies: text: Sorry I did not take part in these "ad nauseam" discussions. I am a mere reader of the French news speaking about your project of using Wikipedia to share knowledge on human genes. When I click on http://www.pdb.org , what strikes me is "© RCSB Protein Data Bank" at the bottom of the page. So, if they have a specific page mentioning the fact that they release all or part of their images in the public domain, it would be better to provide a link to that page (in my humble opinion), in addition to the specific page where the picture first appeared (rather than the pdb.org homepage) (is it http://www.rcsb.org/pdb/explore/images.do?structureId=1LUI ?). An other question/suggestion is : why don't you upload these pictures on commons ? As explained on Help:Images and other uploaded files, uploading images on Commons helps wikipedias in all languages to share pictures. Teofilo talk 14:20, 11 July 2008 (UTC)
replies: text: Link that states the data availability: http://www.pdb.org/robohelp_f/#site_navigation/citing_the_pdb.htm  "Data contained in the RCSB PDB are free of all copyright restrictions and made fully and freely available for both non-commercial and commercial use...." with some more details at that link. Mary Mangan (talk) 19:52, 11 July 2008 (UTC)
replies: text: Thank you. Here-is a non-flash link  http://www.pdb.org/robohelp_f/site_navigation/citing_the_pdb.htm . It looks OK regarding copyright, but « Users of the data should attribute the original authors of that data ». Do we know the names of the original author(s) of :Image:PBB Protein ITK image.jpg ? Teofilo talk 10:01, 12 July 2008 (UTC)
replies: text: In talking with the RCSB folks, I think we determined that the images themselves are created by the PDB, hence the "attribution" to www.pdb.org.  You're right that a link directly to the specific PDB entry would be more precise and an even better service to our users.  I've added it to our to-do list.  Regarding uploading to wiki commons, yes this is something that was also brought to our attention.  We can clearly do this with the expression images that we generate, but I'd need to make absolutely sure that the wiki commons license and RCSB licenses are compatible.  (I think we did conclude that earlier.  more context here.)  Thank you for these suggestions.  Cheers, AndrewGNF (talk) 16:17, 12 July 2008 (UTC)
thread_title:  [[:Image:PBB Protein ITK image.jpg]] 

message: 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)
replies: text: Ahh, great point...  Thanks for the heads up, and we'll see about the best way to fix that...  Cheers, AndrewGNF (talk) 13:45, 9 July 2008 (UTC)
replies: text: Possibly related bug:  when I was on the c3orf58 page I clicked the RefSeq link (which goes to UCSC, would have expected it to go to NCBI).  Anyway--since I had been on the mouse genome earlier at UCSC, this RefSeq number searched the mouse genome and linked to the mouse browser.  So that same RefSeq link could search human if you had been on human, mouse if you had been on mouse, and it even searched Lizard for that when I went over and was using lizard prior to clicking.  Is this where bug reports go?Mary Mangan (talk) 20:33, 11 July 2008 (UTC)
replies: text: Hi Mary, unfortunately, that older template is not one written by us.  I agree that the refseq link should go to NCBI instead of UCSC, but that change should probably be discussed at Template_talk:Protein.  AndrewGNF (talk) 16:21, 12 July 2008 (UTC)
thread_title:  Mouse location links lack db name parameter 

message: 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 ). 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)
replies: text: Great idea, thanks for the input.  We're a bit bandwidth limited at the moment, but I've added it to our to-do list.  Cheers, AndrewGNF (talk) 15:41, 11 July 2008 (UTC)
replies: text: Wonderful! I suggest reading also other good practices for Wikipedia diagrams like replacing captions in the image with text (see also Wikipedia:Image use policy). Cheers —surueña 11:02, 14 July 2008 (UTC)
replies: text: Thank you surueña, another good suggestion that has been duly noted.  AndrewGNF (talk) 15:42, 14 July 2008 (UTC)
thread_title:  SVG images 

message: 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)
replies: text: Hmmm, the issue of mitochondrial genes and their genome locations hadn't even come up yet.  I made this change for ND6.  I think that fixes it, right?  (except for the mm8/mm9 issue for mouse, which we still need to tackle).  If that looks good to you, then I'll try to go through and get the full list of gene pages that need this update...  AndrewGNF (talk) 16:48, 12 July 2008 (UTC)
replies: text: Yeah, that appears to make the syntax correct.  I think there's a separate issue of the mitochondrial data at UCSC.  I need to ask them about that.  But I'm not available next week, so don't wait for an answer from me before moving on the others. Mary Mangan (talk) 17:14, 12 July 2008 (UTC)
thread_title:  ProteinBoxBot mitochondrial bug 

message: 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)
replies: text: Hi Boghog, do you not see an edit link above the right-side infobox?  These changes were meant to create what you describe above (I think)...  Let me know what behavior you're seeing.  AndrewGNF (talk) 18:21, 24 July 2008 (UTC)
replies: text:  Good grief!  I must be going blind ;-)  You are right, the link is already there.  I guess I never noticed it before.  Sorry about that.  Cheers.  Boghog2 (talk) 18:33, 24 July 2008 (UTC)
replies: text:  No problem at all...  (Keep up the great work BTW!  You are an amazingly prolific editor...)  Incidentally, if anyone feels like helping out, I recently added this link to User:ProteinBoxBot, which shows all edits to pages which contain .  In short, it's a watchlist for the "Gene Wiki".  I think the more eyeballs we have periodically scanning the list (or vandalism, newbie editors, etc.), the better.  AndrewGNF (talk) 19:51, 24 July 2008 (UTC)

text:  Thanks for the heads up on how to view recent changes to Gene Wiki pages. My own watch list covers a small fraction of these pages. It will be interesting to monitor to progress of the project and of couse I will jump in and help where I can. Boghog2 (talk) 11:34, 25 July 2008 (UTC)
thread_title:  Edit link for PBB templates 

message: e.g. with the wikilinks in this edit: http://en.wikipedia.org/w/index.php?title=MAGEA3&diff=227790302&oldid=224566405 be reverted when the summary is updated? Thanks, --Rajah (talk) 07:50, 25 July 2008 (UTC)
replies: text: Hi Rajah. Thanks for your additions to the MAGEA3 article. As explained in , to make sure that your changes to the PBB summary section are not overwritten, you need to change the setting of the "update_summary" parameter from yes to no. The PBB control section is normally at the very bottom of the text in the article's edit window. Cheers. Boghog2 (talk) 11:22, 25 July 2008 (UTC)
replies: text:  ..., and in thinking more about how these gene pages will progress, I think it's also safe to completely remove the PBB_Summary template whenever you make a change (even something as trivial as wikilinking or fixing a typo).  We've always said that any human edits trump a bot edit, and long term, it was always the hope that these summaries from Entrez Gene would eventually just dissolve away into the rest of the text.  The template is good, however, for maintaining the thousands of pages that have yet to be substantially touched, especially those that do not yet have a summary from Entrez Gene (but may get one in the future).  Cheers, AndrewGNF (talk) 14:57, 25 July 2008 (UTC)
replies: text: Ok, yeah, my concern was that more information would be added in the future. So, if I set it on no instead of yes, potential information in the future wouldn't get added. Thanks for the clarification. --Rajah (talk) 05:43, 26 July 2008 (UTC)
thread_title:  Does PBB Summary updates remove changes made to text within them? 

message: 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)
replies: text: Thanx for improving the DQA1 and DQB1 pages. If I can make a recommendation, there should be a special protein box and bot for dealing with  heterodimers, trimers and the like. If this can be done I will convert the old manual boxes I have used to the new style.  The information in the protein box on HLA-DR page is not correct for HLA-DR, it only contains information on the alpha chain, but DR is composed of a beta and alpha chain, I am enclined to revert it to its old protein box since I don't want to tamper with the new template. I modified the old protein template to deal with the issue of heterodimers. For the time being I expanded HLA-DRA from a redirect page and placed the DRA page. I have replaced the illustration on the HLA-DR page, and moved the illustration of HLA-DR1 to the HLA-DR1 page.  One thing that can be done and I wanted to do but did not have the time. Some of these DR  pdb images are of different isoforms, if we could have one isoform pdb mentioned on the HLA-DR page, and one isoform pdb on its appropriate HLA-DRx page then that would take some of the trivial information off the protein-box. These long protein boxes and interfere with other picture placements on the pages, so that reducing trivial information in the boxes is a good thing.PB666 yap 17:04, 27 July 2008 (UTC)

text: [I should point out that HLA-DR is not 1 heterodimer but 3 heterodimers, αβ1, αβ3, αβ4, αβ5 with the beta chains encoded by 4 separate genes HLA-DRB1, HLA-DRB3, HLA-DRB4, HLA-DRB5 It may be best to manually style the protein box for HLA-DR, and have separate boxes for each of the above-linked pages. And why is HLA-DRB4 called HLA-DRB4 (gene)?]PB666 yap 17:04, 27 July 2008 (UTC)
replies: text:  Hi. Thanks for your contributions to the HLA-DQA1 and HLA-DQB1 articles.  My edits to the these articles were done before I read your questions above.  The PBB summary templates may be a little confusing and/or intimidating initially, but they are in fact designed to be edited. As mentioned above, if you do make changes to this section, please be sure to change the value of the "update_summary" parameter from "yes" to "no" so that your edits are not over written by automatic bot updates. Concerning heterodimeric proteins, may I suggest that we leave the existing gene/protein specific articles in place and create a new article for this gene family and include a section discussing the composition and properties of these heterodimers.  This gene family page could contain the old-style  boxes (which are more compact than the PBB template) for each of the four genes. Cheers. Boghog2 (talk) 18:51, 27 July 2008 (UTC)
replies: text:  Per the discussion above, I went ahead edited the HLA-DR article to replace the single  template that only contained information about the HLA-DRA gene with five more compact  templates which include information about the entire gene family (HLA-DRA + HLA-DRB1 + HLA-DRB3 + HLA-DRB4 + HLA-DRB5). Is this OK? Boghog2 (talk) 20:12, 27 July 2008 (UTC)
replies: text:  I went to look at previous versions of the HLA-DR article and now I can see where the problem originated.  You already had a nice compact protein box that contained information about all five gene/proteins that at one point was replaced with a  template containing information only about the HLA-DRA gene. This was a mistake.  The HLA-DR article should have been left as is and the  template should have been added to the HLA-DRA article. I hope this clarifies things (at least it clarifies the problem for me ;-). Cheers. Boghog2 (talk) 20:54, 27 July 2008 (UTC)
thread_title:  The protein boxes 

message: 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)
replies: text: Done. Tim Vickers (talk) 16:40, 14 August 2008 (UTC)
thread_title:  Image copyright problem with Image:PBB Protein NFAT5 image.jpg 

message: 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)
replies: text: Done. Tim Vickers (talk) 16:41, 14 August 2008 (UTC)
thread_title:  Image copyright problem with Image:PBB GE TLK2 212986 s at fs.png 

message: 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)
replies: text: Hi CopperKettle, sure, no objection from our end.  As to the best technical way to do it, I'm not sure.  I suppose you could just download the source from the protein box template (for NOTCH1, this lives at Template:PBB/4851).  If you were going to do it programmatically, you might even use the special:export function (e.g., ).  Hope that helps...  AndrewGNF (talk) 15:40, 19 August 2008 (UTC)

text: ... and by the way, you may or may not have noticed, every time someone asks me why we did the Gene Wiki project, I hold up Reelin as an example of what each page could become.  (e.g., , , )  Anyway, seeing as how you played a big part in developing that page (and completely prior to our effort), I hope you take some pride and satisfaction in that...  Cheers, AndrewGNF (talk) 15:47, 19 August 2008 (UTC)
thread_title:  Is it possible to copy the contents into another language Wiki? 

message: 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)
replies: text: I see this issue was discussed in the past. Unfortunately, the statement that "the "CD38 molecule" is a special case" is utterly false. There are hundreds, probably even thousands, of articles that incorrectly state that a certain protein is in fact a gene. This is not "minutae". This is not unimportant. This is a ubiquitous trait of pages created with the ProteinBoxBot. It's rather strange that a bot with such a name would mostly create pages about "genes". If the majority of the articles the bot creates are factually erroneous, perhaps it would be best for the community not to have such a bot. I'm not entirely against it, but from what I've seen, it needs work at the very least. (Another consideration is the "jargon issue", brought up in the past. Not only in regards to biology jargon, but the technical jargon that the bot inserts in articles as a marker/controller.) Fuzzform (talk) 00:13, 2 October 2008 (UTC)
replies: text: I don't see the problem with GPR3, Entrez lists this as a human gene (link), is the problem that this is a gene in other organisms as well? Tim Vickers (talk) 02:23, 2 October 2008 (UTC)
replies: text:  I couldn't resist expanding the GPR3 article.  How does it look now?  Obviously as noted before, these pages are about both the gene and the protein. The gene is named after the protein, so as Tim points out above, it is not incorrect to refer to GPR3 as a gene, although to be completely correct GPR3 (note italics) refers to the gene and GPR3 (non-italicized) to the protein. The first sentence of the lead which implies that these articles are about genes is at worst incomplete but certainly not incorrect. The discussion about the "CD38 molecule" was really about two issues.  The first was the strange yet official name given to the CD38 gene/protein and the second was whether the article was about the gene or the protein.  The former as Andrew points out is a special case, the later, as you point out applies to all the articles.  I hope this clarifies things. Cheers. Boghog2 (talk) 19:07, 2 October 2008 (UTC)
replies: text: I don't think there is a case for having articles on both a gene and its products and I'm personally happy with having an article that discusses both - since most of the material will be common to both. Tim Vickers (talk) 20:05, 2 October 2008 (UTC)
replies: text:  I absolutely agree that in the vast majority of cases, we should keep the gene and corresponding protein(s) together on one page.  Boghog2 (talk) 21:14, 2 October 2008 (UTC)
replies: text:  Agreed Fuzzform, it's poor wording.  If we had to do it over again, we should probably do something like "G protein-coupled receptor 3 is a protein which in humans is encoded by the GPR3 gene".  But, for all the exhaustive oversight (by WP:BAG, WP:MCB, etc.) of the bot prior to its mass runs, that one just slipped under the radar.  Anyway, as Tim and Boghog have pointed out, the consensus was absolutely to keep information on the genes and their corresponding proteins on the same page, so I don't think we have a huge problem here.  And, as always, anyone who feels like helping out fixing this issue (either one-by-one manually or by writing a bot), please feel free...  Finally, as you've undoubtedly noticed, PBB itself is on indefinite hiatus while we search for another willing student.  Cheers, AndrewGNF (talk) 23:47, 2 October 2008 (UTC)
replies: text: I wasn't arguing for separate articles for gene/protein information, I just think that a better (standard) opening sentence is in order for these articles. It is unfair to the vast majority of readers for us to simply assume that it is self-evident that an article is about both a gene and a protein. This needs to be said explicitly, not merely implied. Also, in regards to the gene qualifier "human", we can't assume that the average person knows that, for example, "GPI" refers to the human gene, whereas "Gpi" refers to the gene in other species. This is esoteric information. Even if stating such information in every article seems "excessive and overly pedantic", it is preferable to having articles that are incomprehensible to the majority of readers. A very basic rule when writing non-fiction is to never assume that the reader knows what you know - if they did, why would they be reading at all? Which leads me to another point... these gene/protein articles do not (or at least, should not) constitute a reference work for experts in the field. This seems to be where the "self-evident information" fallacy comes from. Anyway, my point is this: Never assume that information is self evident; always state it explicitly. Fuzzform (talk) 19:03, 6 October 2008 (UTC)

text:  ... ooh, and just noticed on your userpage that you're a beginning python programmer.  Interested in getting your feet wet with a little bot programming?  Nothing like real-world experience for learning to program... AndrewGNF (talk) 23:50, 2 October 2008 (UTC)
replies: text: Sure, I'm always interested in learning something new. Just point me in the right direction. Fuzzform (talk) 19:03, 6 October 2008 (UTC)

text: Fuzzform, you still interested in doing some bot programming for the Gene Wiki project?  If so, I'd suggest two possibilities.  First, we could take the topic that you've highlighted above -- the poorly worded first sentence.  I could give you the index of pages in the Gene Wiki, you could programmatically see if that ugly first line exists, and if so, we could change it to something better.  Of course, we'd want to agree on what it should be changed to here, but I can't see that being a big obstacle.  The second idea is one that I've been very excited about but have yet to find someone help achieve it.  I'd like to create a master chart that tracks Gene Wiki growth and progress (what Edward Tufte calls a "supergraphic").  Basically, it involves going through the history of all Gene Wiki pages and tracking each page by time and size.  Phase II would be converting all that data into an SVG graphic.  Anyway, either of these projects I bet would be a good way to hone your python skills.  Let me know if either of those strike your fancy (or if anyone else lurking is interested...)  Cheers, AndrewGNF (talk) 00:18, 12 October 2008 (UTC)
thread_title:  Protein vs. Gene 

message: 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)
replies: text: Thanks for the feedback.  Yes, it's on our to-do list to get all PD images (expression and PDB) over to wikicommons.  Unfortunately, still hunting around for a willing student...  (As noted above, any coders who want to take on this challenge, please let me know.  In return, you get some good experience, and if your contributions are reasonably substantial, co-authorship on the next gene wiki paper...)  AndrewGNF (talk) 06:46, 9 October 2008 (UTC)
thread_title:  Uploding on Commons 

message: 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)
replies: text: Thanks for your contributions to Gene Wiki articles.  In order to make sure that your edits are not overwritten in a future automatic update, the only thing you need to do is turn off the PBB summary update parameter as for example in this edit.  This has been documented on the Portal:Gene_Wiki page (General FAQ, item #2). Also if you turn of the automatic update parameter, feel free to remove the template itself ( the text "" that surrounds the summary) as for example in this edit, since it is no longer needed. Cheers. Boghog2 (talk) 09:45, 31 December 2008 (UTC)
replies: text: Problem is, I don't feel competent to make the decision to switch off automatic updating, just because I have found a little link that should be made. I don't know what the benefits of automatic updating are. Further the existence of the Portal and FAQ is not transparent to the editor, who is only directed to Template:PBB Controls. Editing these pages is quite intimidating. AxelBoldt (talk) 15:39, 31 December 2008 (UTC)
replies: text: Hi AxelBoldt, one of our fundamental principles behind the Gene Wiki is that any human edit is more competent than a bot edit.  The benefits of automatic updating of the gene/protein summary are far outweighed by attention from human eyes (even adding a wikilink), so you should feel free to do as you see fit.  The automatic updating is primarily aimed at the vast majority of pages that haven't yet been edited by a human, just to keep them in sync with the source databases.  Agreed, the instructions are a bit more convoluted and intimidating than they need to be, which is why Boghog suggested that you simply remove template markings once you make any sort of edit.  In the future, we're hoping to simplify the pages even more (but suffering from lack of bandwidth at the moment).  Cheers, AndrewGNF (talk) 17:58, 31 December 2008 (UTC)
replies: text: If human edits are indeed seen as more important than bot edits, you could simply instruct the bot to only update protein descriptions that haven't been altered since the last bot update round. (The other ones should be added to a list for human review.) AxelBoldt (talk) 16:14, 2 January 2009 (UTC)
replies: text: The short answer is that we'd like to do that, but technically it's non-trivial to determine if the summary has been touched.  The easy thing to do is that if there's any evidence of changes (e.g., wikilinks), then the bot will not update.  (So, you can assume that adding a wikilink is the same as turning off the summary.)  We may even go a step further and say that any non-blank summary will never be updated by the bot.  Anyway, right now, these are all theoretical discussions since we don't have a primary PBB developer at the moment...  (volunteers?)  Cheers, AndrewGNF (talk) 00:52, 3 January 2009 (UTC)
thread_title:  Linking terms in protein summary? 

message: The portal uses two templates to generate new paragraphs:
* box 2 if there is a content, and box 1 if only a title is needed. 
* Due to this change by Andrew I made this change to correct paths for a solution via weblinks. The page "Facilites" should look correct now. 
* If there are new boxes please change/add/strike the overview in Portal:Gene Wiki/Sitemapping.
Thx! Simplicius (talk) 12:48, 6 August 2008 (UTC)
replies: text: Ahh, thanks for that catch and fix...  I like the link directly to the edit page because I think it's a bit clearer to the newbie.  The concepts of templates and transclusions are somewhat advanced, and I can see a newbie editor being confused if the "edit" link just goes to another wiki page.  (BTW, sorry for the late replies -- was out of town last week...) AndrewGNF (talk) 18:49, 12 August 2008 (UTC)
thread_title: Template Box 1 and 2

message: Link - very cool. Tim Vickers (talk) 02:19, 4 September 2008 (UTC)
replies: text: I'm really chuffed that they mention PDBWiki :-D --Dan|(talk) 14:02, 4 November 2008 (UTC)
thread_title: Nature article

message: 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)
replies: text: Well, we've been really rethinking how the overall flow of the program works (including how updates are handled) so those documents became a bit obsolete.  Really I think the thing worth reporting is not the program, but the output of the program.  Open to being convinced otherwise though...  AndrewGNF (talk) 15:21, 4 November 2008 (UTC)
thread_title:  About the Bot? 

message: 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)
replies: text: Thanks for your comment.  Based on the discussion  here, an enhancement where "" is replaced with "" has been added here.  The advantage of this solution is the number of columns displayed in dynamically adjusted depending on the screen width.  If the width is narrow, only a single column is displayed.  I have made this change to the ST3GAL3 article.  Does this look OK?  Cheers.  Boghog2 (talk) 15:13, 30 April 2009 (UTC)
thread_title: Double column

message: 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)
replies: text: The most recent discussion was here (toward the bottom of the archive).  Cheers.  Boghog2 (talk) 19:53, 30 April 2009 (UTC)
replies: text:  Super, thanks much!  AndrewGNF (talk) 21:21, 30 April 2009 (UTC)
thread_title:  PBB lead discussion

message: 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)
thread_title:  Relating gene pages by protein interactions 

message: 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)
replies: text: And it does not seem to be going so well :) Fvasconcellos (t·c) 00:31, 28 July 2009 (UTC)
replies: text: One more:  Fvasconcellos (t·c) 00:31, 28 July 2009 (UTC)
replies: text: Any more?  I'm not sure what happened on those two pages, but it seems to be going fine for the other pages.. JonSDSUGrad (talk) 00:59, 28 July 2009 (UTC)
replies: text: Yes, quite a few; see my recent contribs. Fvasconcellos (t·c) 01:03, 28 July 2009 (UTC)
replies: text: Ok, I found the bug.  I've stopped the bot and hopefully not too much damage has been done.  After the reverts are done I'll start it back up. JonSDSUGrad (talk) 01:08, 28 July 2009 (UTC)
replies: text: Glad you found it. Fvasconcellos (t·c) 01:27, 28 July 2009 (UTC)

text: The problem will occur on any page missing the refend template.  If there is an easy way to cross reference the edits made yesterday with pages that are missing the template, we should find all the errors. JonSDSUGrad (talk) 18:33, 28 July 2009 (UTC)
replies: text:  Update - Thanks to those that helped revert pages damaged by the bug (there were 29 pages damages, now all fixed).  The run was otherwise successful with about 2800 pages being updated with the PDB Gallery.  JonSDSUGrad (talk) 22:35, 30 July 2009 (UTC)
thread_title: Protein Box Bot Update

message: A request for comment has been made at the above link.  Your input is welcome.  Boghog2 (talk) 20:32, 19 August 2009 (UTC)
thread_title:  [[Wikipedia_talk:WikiProject_Pharmacology#Proposal_to_link_to_external_IUPHAR_database|Proposal to link to external IUPHAR database]] 

message: :: Discussion moved from User_talk:TimVickers:
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)
replies: text: Sorry for butting in, but I think many of the changes from cytogenetic band to megabasepairs that you refer to were due to replacing  with  templates. The megabasepair location was used to provide  a link to the UCSC Genome Browser. The advantage of the megabasepair link is that it more precisely targets the gene in question (one-to-one relationship) whereas one cytogenetic band may contain more than one gene (one-to-several relationship).  I believe situations where "N/A" is displayed is due to omissions in the data file where these gene locations were obtained (ftp://ftp.ncbi.nih.gov/gene/DATA/) and we are slowly fixing these omissions as we find them. I hope this clarifies things.  Cheers.  Boghog (talk) 15:07, 4 September 2009 (UTC)

text: Thanks, that clarifies it.   I'm not much good at editing, but is there anything I can do to help?doctorwolfie (talk) 19:51, 4 September 2009 (UTC)
replies: text:  Help is certainly welcome :-)  You can start by letting us know if you find missing data. If you are inclined to do-it-yourself, follow the PBB edit link on the top right hand screen right above the protein box.  This will take you to the transcluded PBB template were you can add the missing data.  If the human gene location is listed as N/A, then you will need to add data to the Hs_GenLoc_chr, Hs_GenLoc_start, and Hs_GenLoc_end parameters.  I get these by following the Entrez Gene link and on the Entrez page, follow the "see related" link to the Ensembl database entry.  The top of the Ensembl page will list the gene location.  There may be easier ways to do this, but this is the only way I know.  Hope this helps.  Cheers. Boghog (talk) 20:31, 4 September 2009 (UTC)
replies: text: Thanks guys...  If you prefer, you can also use the tool described here to update the entire PBB template, under the assumption that most of the NAs have since been resolved.  If that's not the case, and you start noticing more than a few of these, then perhaps we should start assembling a list so I can track down what's happening here.  Cheers, AndrewGNF (talk) 21:50, 4 September 2009 (UTC)
thread_title:  Gene Locations 

message: 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)
thread_title:  Help finding edits which could be candidate GO annotations 

message: 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)
replies: text: On second glance, following the actual proposal to add SCOP classification as a category seems best and should take first priority.  If others like my above suggestions about where to add the classification, those can be done as well. Emw (talk) 16:21, 4 November 2009 (UTC)
replies: text:  Hi, Emw.  The first version of this project was completed previously.  We uploaded 66,000 PDB thumbnail images to commons and categorized according to SCOP.  You can browse the collection at http://commons.wikimedia.org/wiki/SCOP.  Of course, if you want to amend or replace those images with your higher-quality versions, go for it.  You can use the existing category structure as a guide.  Also, SCOP I'm sure has a downloadable file, so you won't need to hit their web server repeatedly.  Cheers, AndrewGNF (talk) 21:06, 4 November 2009 (UTC)
thread_title:  Adding SCOP classification 

message: 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)
replies: text: Impeccable timing.  In the same minute that you posted your note, this change was made to  that fixed that problem.  There was a slight delay in fixing it because the template is protected (only admins can change it).  In any case, let us know if you notice anything other bugs...  Cheers, AndrewGNF (talk) 15:50, 9 October 2009 (UTC)
replies: text: Now that's what I call an efficient service! --Paul (talk) 21:34, 9 October 2009 (UTC)
thread_title:  PBB bug or feature? 

message: 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)
replies: text: These integrins appear to be heterodimers composed of two different proteins encoded by two seperate genes. The α4β7 integrin is composed of CD49d (α4) and ITGB7 (β7) proteins while Alpha-v beta-3 is composed of ITGAV and CD61. Cheers. Boghog (talk) 11:45, 14 October 2009 (UTC)
replies: text: Oh, yes, how stupid of me :-) --ἀνυπόδητος (talk) 11:48, 14 October 2009 (UTC)
thread_title: Which integrins are that?

message: 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)
thread_title: Glycoprotein 72

message: 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)
replies: text: I have taken the liberty of correcting this myself. Newly uploaded image should be of 1fxl. best, Sunil060902 (talk) 17:24, 27 October 2009 (UTC)
replies: text:  Thanks for the explanation and for correcting the error. Cheers.  Boghog (talk) 19:05, 27 October 2009 (UTC)
thread_title: [[HuD]]/ELAVL-4

message: 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)
replies: text: This was a case of vandalism which I have reverted.  Thanks for pointing it out.  Cheers.  Boghog (talk) 07:54, 16 November 2009 (UTC)
replies: text:  To the bot template? --The New Mikemoral ♪♫ 06:37, 20 November 2009 (UTC)
replies: text:  Sorry for not being clearer.  The bot did not introduce the full chemical name.  The name was introduced by User:Teqnique in this edit. As you can see in the history of the  template, it has been vandalized several times by different human editors and in each case, the vandalism was reverted. Boghog (talk) 10:16, 20 November 2009 (UTC)
replies: text:  Ah, that makes sense. --The New Mikemoral ♪♫ 01:57, 21 November 2009 (UTC)
thread_title: [[Titin]]

message: 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 ? --ἀνυπόδητος (talk) 12:36, 16 November 2009 (UTC)
replies: text: The official HUGO gene name and UniProt protein name are both epithelial cell adhesion molecule.  So I suggest that the name of the tumor-associated calcium signal transducer 1 be changed to "epithelial cell adhesion molecule" and the material from EpCAM be merged into the newly renamed article.  Does this sound reasonable?  Cheers.  Boghog (talk) 22:04, 16 November 2009 (UTC)
replies: text: Yes, that sounds good. I did the move, but have no time for the merge at the moment. Also, I'm not sure what to do with the PBB Summary template. Could you do that? Cheers --ἀνυπόδητος (talk) 07:20, 17 November 2009 (UTC)

text: Fine – does that mean, just remove the PBB Summary in favour of a human-written article? --ἀνυπόδητος (talk) 18:19, 17 November 2009 (UTC)
replies: text:  Hi ἀνυπόδητος, in general, those PBB Summary templates should be removed at whatever point they cease to be useful.  Normally they were added to pages that had no other free-text content, so it was just meant to be a starting point.  Cheers, AndrewGNF (talk) 20:40, 17 November 2009 (UTC)
replies: text: Thanks! --ἀνυπόδητος (talk) 09:04, 18 November 2009 (UTC)
thread_title: [[Tumor-associated calcium signal transducer 1]]