User talk:ProteinBoxBot/Archive2

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more identifiers

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)

For the record, i found this discussion. David D. (Talk) 06:03, 5 February 2008 (UTC)
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)
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 Biophys (talk · contribs), he seems to have been the one to code this box? David D. (Talk) 06:17, 5 February 2008 (UTC)
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)
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)
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)
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)
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)
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)
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)
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)

google ranks

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)

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)
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)
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)

Sources

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)

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)
Cool, thanks! And sorry I missed the last section! -- Lea (talk) 21:49, 8 February 2008 (UTC)

We need genes here

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)

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)

Simply not Public Domain

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.[1]

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)

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)

Done. Tim Vickers (talk) 18:18, 6 February 2008 (UTC)

I think the final decision on this was that we need to use the {{attribution}} tag rather than {{PD-release}}. Tim Vickers (talk) 17:34, 10 February 2008 (UTC)

Unspecified source for Image:PBB_GE_NIPA1_gnf1h07157_at_fs.png

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)

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 {{self}}, 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 {{cc-by-sa-3.0|[[Genomics Institute of the Novartis Research Foundation]]}}, 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)
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)
The data come from this article: PubMed. Should the article itself then be listed as the source? AndrewGNF (talk) 02:21, 8 February 2008 (UTC)
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)
Super, thanks much... AndrewGNF (talk) 05:56, 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)

 ;) I don't envy your job (if one can call it a "job"...) AndrewGNF (talk) 06:07, 8 February 2008 (UTC)
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)

doi weirdness

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)

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)

Not {{Attribution}}, either

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)

For whatever it's worth to you, see {{PDB}}. Stephen Ewen (talk) 06:52, 13 February 2008 (UTC)
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)

Integration between enzyme and gene pages

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)

(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)

Newline layout issue in created articles

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)

Thanks, fixing this issue for newly-created pages is definitely on our to do list. Cheers, AndrewGNF (talk) 00:54, 17 March 2008 (UTC)
Okay, great! Melchoir (talk) 17:37, 19 March 2008 (UTC)

GO terms - internal links

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)

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)

Protein pictures

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)

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., [5]). (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)

Image copyright problem with Image:PBB GE PPP4R1 201594 s at tn.png

Image Copyright problem

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)

Fixed! Thanks... AndrewGNF (talk) 22:18, 2 April 2008 (UTC)

Image copyright problem with Image:PBB GE DMTF1 203301 s at tn.png

Image Copyright problem

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)

Fixed! Thanks... AndrewGNF (talk) 22:17, 2 April 2008 (UTC)

Fault

There is a fault with SLC47A2 -wrong name at the beginning ♦Blofeld of SPECTRE♦ $1,000,000? 17:32, 9 April 2008 (UTC)

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)

Possibility of implementing wikilinks in the PBB Summary?

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)

Good idea! One could link automatically only first instance of the "biological" word in the article to avoid "overlinking" and include in the vocabulary Latin names of species, names of proteins, etc. I posted such proposal to "bot proposal" page, but no one liked the idea. Actually, User:Banus did linking of Latin names of species when he made a semi-prep InterPro file which I used (see wikified names in article Gamma thionin for example - that was done automatically).Biophys (talk) 21:49, 10 April 2008 (UTC)
That was easy: the names of species are enclosed in a "taxonomy" tag, and you only need to convert the tag into the familiar square bracket (an easy string substitution). A more general solution requires the construction of an (article, aliases) table automatically or from user-provided data, a pretty good parser (don't grab locution having a comma within, for example), greedy match (always find the longer locution corresponding to an article) and in general a good heuristic to avoid overlinking and resolve name conflicts. This isn't a impossible task, but it require a little more work than pattern matching and string substitutions ;) The bot developer (JonSDSUGrad (talk · contribs)) said something about it here. —Banus (talk) 22:48, 10 April 2008 (UTC)
First, regarding the bot overwriting. Yes, I still believe that user-contributed content (even as minor as wikilinking) should generally trump any sort of automated updates from Entrez. In fact, for people who are editing the text in the PBB_Summary template in any way, feel free to strip away the surrounding template completely. Regarding automatic overwriting, I'm thinking before our next genome-scale run, I want to look for the presence of any wikilinking in the PBB_Summary, and if found, PBB would automatically turn its own update_summary flag to "no". After all, not everyone should be expected to realize that they have to actively turn that flag off. So that addresses the issue regarding overwriting human contributions...
Next, the issue of auto-wikilinking. It's a reasonable idea with a few limiting factors (solutions to which may be feasible with a little discussion here).
  1. First, it's not a trivial task to create the dictionary of biological terms. It's not a project that I have any special insight on for either doing it manually or in some automated way.
  2. Second, auto-wikilinking also complicates the plan above for avoiding the stomping of human edits. I think implementing auto-wikilinking would mean (practically speaking) the end of auto-summary updates (except for the case where the summary is initially blank). I just can't think of a good way to avoid human edits if we take away the assumption that all wikilinks are human-generated.
  3. Third, we have an overabundance of good ideas and an underabundance of people to implement them. Speaking of which...
It seems appropriate at this point to publicly congratulate JonSDSUGrad on the successful defense of his Master's thesis project. Unfortunately, that also means that we may be losing his focused efforts shortly. For those who have been interested, I've been generating a list of discrete projects here for the next student (still to be found), but actually I'd really like to expand this beyond a one-developer effort. If you know of someone (or are someone) who might be interested in directly contributing to PBB, please let me know. Cheers, AndrewGNF (talk) 22:58, 10 April 2008 (UTC)
Congratulations! As an example of human gene coverage, one can look at the list of human genes in Pleckstrin homology domain. This list was generated automatically from UniProt. A few extra runs by the bot would be great.Biophys (talk) 18:39, 11 April 2008 (UTC)
I've done a few searches based (loosely) on the redlinks in Pleckstrin_homology_domain#Human_proteins_containing_PH_domain and posted the results here: User_talk:ProteinBoxBot/Pleck. First column is the rank (by number of citations in Entrez Gene), second column is Entrez Gene ID, third column is number of citations, and fourth column is gene symbol. Recall that PBB was approved for doing the top 10K ranked genes for notability reasons. There are about 800 or so "tough cases" left that I'll be dealing with soon. Although all the PH domain redlinks that I checked fall below the 10k threshold, I'm always happy to do requests by protein family if you can provide the Entrez Gene ID and the correct target page. Easiest place to put it is in User:ProteinBoxBot/Requests. Cheers, AndrewGNF (talk) 21:17, 11 April 2008 (UTC)
I am sorry for arguing here, but this artificial cutoff has not justification whatsoever. As long as we can provide a couple of sources, an article belongs to WP per WP:verifiability. I looked through the most recent log (April 10). All included articles are sourced pretty well, some even have a PDB picture. I would definitely include all genes that have either an Entrez Gene abstract (at least a couple of phrases) or a PDB structure. I also do not see any reason why not to include all genes with at least 3-5 references.Biophys (talk) 02:49, 12 April 2008 (UTC)
10K was a conservative target so that we'd be reasonably sure that all pages would be pretty assuredly notable. I agree with you, we can probably go lower down the list. But I'm erring on the side of treading cautiously so that no one will accuse PBB of being too rash. Once we get the 10K run completely done, then I'll propose another task at the WP:RBA and I'll look for your enthusiastic support there. In the mean time, you're welcome to post your favorite genes on the requests page or just sit tight for now... Cheers, AndrewGNF (talk) 04:56, 12 April 2008 (UTC)
Agree. I like this project a lot. It has been a great success. Thank you, JonSDSUGrad and others for doing this!Biophys (talk) 06:30, 12 April 2008 (UTC)