Wikipedia talk:WikiProject Molecular Biology/Gene Wiki/Archive 1

message: Would it be possible to create a references section on the page using the bibliography data in the Entrez gene page? TimVickers 22:41, 4 May 2007 (UTC)
replies: text: Great ideas, added it to the specs.  I propose adding any gene with either a gene2pubmed entry (minus the genome-wide annotation papers that are linked to tens of thousands of genes) or a generif.  sound good? AndrewGNF 18:10, 5 May 2007 (UTC)

text: Whoa, great discussion I've been missing out on!  Looks like lots of good feedback and ideas there contributed in a very short amount of time.  Anyway, thanks for the pointer and starting the thread.  I'll be sure to chime in... AndrewGNF 22:58, 7 May 2007 (UTC)
replies: text: Since Tim Vickers' reference to the Village Pump discussion (above) has timed out, I replaced it with a history pointer. EdJohnston 19:38, 25 June 2007 (UTC)
thread_title:  Idea 

message: One of the planned outputs of this project is a peer-reviewed publication, and it would be nice to include in that publication some metrics of ProteinBoxBot's impact.  Some ideas:
* Obviously, simply the number of articles created or edited by PBB
* the number or pre- and post-PBB edits by other users (say, within a +/- one-month time frame)
* the number of wikilinks per article (either to other PBB pages or to other WP pages as a whole)
other ideas? AndrewGNF 17:17, 21 September 2007 (UTC)
replies: text: But what is the subject/title of your publication? Is it "Curated database of human protein expression profiles", or is it "Using Wikipedia as a collaborative tool for annotation of human genome"?Biophys 14:26, 7 November 2007 (UTC)
replies: text: Something more along the latter.  The former have already been published here and here. AndrewGNF 17:54, 7 November 2007 (UTC)
replies: text: Good luck! It would be interesting to look at your article. I think this will also provide some good publicity for WP.Biophys 04:18, 9 November 2007 (UTC)
thread_title:  evaluation metrics 

message: Is copyright status of Entrez Gene compatible with Wikipedia, so we can copy anything from there?Biophys 00:20, 4 November 2007 (UTC)
replies: text: Most notably, OMIM content is not.  Sigh, it would be great to use that content to seed the free-text section.  (If OMIM were *really* smart, they'd just convert their own site over to a wiki, but I hear NCBI wants nothing to do with public wikis...) AndrewGNF 03:27, 5 November 2007 (UTC)
thread_title:  Entrez Gene 

message: Wow, it is already going after pseudogenes - see HCG4P11. Should not they be filtered out and perhaps included into a separate List of human pseudogenes?Biophys 17:43, 4 November 2007 (UTC)
replies: text: Ooops.  It was definitely not our intention to go after pseudogenes.  In case you're wondering, the order so far has been determined by the number of linked citations in Entrez Gene.  (The top of the list are all the classics -- p53, VEGF, TNF, EGFR, etc...)  I think this particular case is related to some server hiccups we've been having over the weekend.  In fact, we've had to temporarily stop automated edits while we look into it.  Anyway, to sum up, psuedogenes are generally not high on the priority list... AndrewGNF 03:39, 5 November 2007 (UTC)
thread_title:  Pseudogenes 

message: The bot did not pick up PDB image for MUC1 for some reason... It also did not identify UniProt link for Peptidylprolyl isomerase A. This suppose to be P62937: .Biophys 23:34, 5 November 2007 (UTC)
replies: text: The image thing looks like a bug -- I've asked JonSDSUGrad to check it out and report back here.  The Uniprot issue looks to be just an artifact of working off of downloaded snapshots of NCBI data (rather than screenscraping their site).  (And working from a local mirror is necessary since we also have to organize all the relationships from so many different sources.)  Right now, our local mirror is a couple of months old.  In the future, we hope to have things a bit more streamlined so we can reduce the lag time between the primary data updates and what PBB sees. AndrewGNF 00:14, 6 November 2007 (UTC)
replies: text: I'm looking into this now - it is strange to me that things did not work correctly, But I will figure out the reason and then correct it if I can. JonSDSUGrad 00:56, 6 November 2007 (UTC)
replies: text: OK. I think I know what happened in this case - it was not so much a bug, but more like an error on my part.  I think I had aborted an update batch in the middle and while the image was uploaded in the aborted instance. PBB was unable to find that it had previously uploaded the image (it already existed) because it was unable to find the created page - I have accounted for this small bug in the code and hopefully something like this will not happen again. It was more of a fluke really, and should only have affected that one log of proteins.  If something like this happens again, it is likely that the image does exist on the wikiserver and you just need to manually write the name of the image file in (I use a standard naming scheme).  If there is any trouble I can also just run pbb for the affected pages again and that should clear them up. JonSDSUGrad 01:28, 6 November 2007 (UTC)
replies: text: The image was not loaded in PLCG1, TIMP1, and PARP1.Biophys 01:42, 6 November 2007 (UTC)
replies: text: Fixed... AndrewGNF 02:18, 6 November 2007 (UTC)

text: MAP4K1 does not have any references, although they are present in Enrez Gene entry. I am not sure how your bot selects references.Biophys 15:10, 6 November 2007 (UTC)
replies: text: There was quite a debate over how to do references during the bot approval process.  I think we settled on linking review articles only that were linked at NCBI.  I don't think we set an arbitrary upper limit in terms of number.  Check out Apolipoprotein_E#Further_reading. AndrewGNF 17:22, 6 November 2007 (UTC)
replies: text: Does it mean that MAP4K1 lacks any references because none of the references in NCBI was a review article? Then you should allow incorporation of at least two non-review references in each created article. Otherwise, anyone can mark articles like MAP4K1 for deletion per WP:Notability. At least one (but better two) references must be present. I would definitely include all references to articles published in Nature, Science, PNAS and Cell as most reliable sources per WP:Source and presumably most highly cited. Biophys 17:43, 6 November 2007 (UTC)
replies: text: Good point.  Added it to the PBB/Ideas page.  If I'm reading the policy correctly though, we could successfully fight deletion because the topic is notable (evidenced by the existence of references), even if the article itself is not (yet) properly referenced.  AndrewGNF 17:58, 6 November 2007 (UTC)
replies: text: Perhaps. But I would recommend to include automatically the references rather than to risk AfD discussions, which is not fun and might negatively affect the entire project. I am an "inclusionist" and do not mind even having articles about pseudogenes, but most people here think otherwise.Biophys 22:48, 6 November 2007 (UTC)
replies: text: Point well taken.  We'll work on it... AndrewGNF 17:56, 7 November 2007 (UTC)

text: It seems that bot sometimes takes an incorrect Uniprot code, as in case of PIAS4 (I fixed it). May be this worth checking.Biophys 05:03, 10 November 2007 (UTC)
replies: text: Hmmm, just took a look and I'm not sure.  PBB linked mouse uniprot to Q3UGQ2, which does link to mouse Pias4.  You changed it to Q8N2W9, which looks like one of the human versions.  PBB linked human uniprot to Q05DS6, which also appears to be reasonable (duplicate entry in Uniprot?).  Can you sanity check me here and let me know if I'm missing something? AndrewGNF 05:24, 10 November 2007 (UTC)
replies: text: Sorry, that is my mistake. I placed code in a wrong place. Q8N2W9 and Q05DS6 are two different human proteins (compare the lengths) but products of the same gene? We definitely need a bot for that kind of work.Biophys 06:29, 11 November 2007 (UTC)

text: PPP2R2A did not pick up UniProt code in the Box. It suppose to be P63151. PPP1CB - same thing. Biophys 16:14, 13 November 2007 (UTC)
replies: text: Just checked, and that association is correctly loaded in our next release of the data.  Feel free to either manually update it now, or just wait until the next update.  Just as proof that keeping links up to date is an incredibly hard problem, note that Uniprot links P63151 to ENSG00000147459, which is clearly not correct.  (Should have been ENSG00000214122.)  Anyway, you can be sure that any portal will have some small percentage of cross-references incorrect at any given time, and ours is no exception...  (The beauty of WP, of course, is that we can override the automatically-computed data with our own human intelligence, which is not possible at any other gene portal).  AndrewGNF 16:56, 13 November 2007 (UTC)

text: ND1 appears in the :Category:Genes on chromosome MT but ND6 and many other proteins do not.Biophys 18:30, 15 November 2007 (UTC)
replies: text: ND6 does for me.  Might have been that the cache is still refreshing on some of these genes?  The easiest way to force a refresh is to edit and save a "blank" edit.  AndrewGNF 19:20, 15 November 2007 (UTC)
replies: text: When you pick :Category:Genes on chromosome MT, do you see ND6 there? I do not.Biophys 19:44, 15 November 2007 (UTC)
replies: text: Ahh, I see what you mean now.  You're right, that seems like odd behavior to me.  Thankfully though, I'm reasonably confident that this is not a PBB bug... ;)  AndrewGNF 20:25, 15 November 2007 (UTC)
replies: text: This is probably related to last update. All articles that do not appear in "Chromosome ..." category have not been recently updated judging from a small set of their journal references. BTW, the articles categorized by the bot do not have normal ":Category:Genes on chromosome MT" record near the bottom. So, I am not even sure where the categories came from.Biophys 02:25, 16 November 2007 (UTC)
replies: text: I think this addition should actually be independent of the PBB doing an update.  Banus previously described how to cleverly add the category to the ortholog template, which I did here.  This should retroactively add the category to all genes with the PBB templates.  Still not sure what the difference is then on why ND1 and ND6 have different behavior... AndrewGNF  —Preceding comment was added at 02:34, 16 November 2007 (UTC)
replies: text: Yes, this was automatically fixed after update. So, one should simply wait until all other articles are updated.Biophys 03:43, 16 November 2007 (UTC)
replies: text: yes, and it can be any update, not just a PBB update.  If you want to force any particular page, just edit and save.  This may be obvious to you and others, but just to be sure...  AndrewGNF 03:50, 16 November 2007 (UTC)

text: The bot generated a very strange category: :Category:Genes on chromosome c6 COX - see pages that belong there. I guess this should be simply chromosome 6.Biophys (talk) 19:10, 20 November 2007 (UTC)
replies: text: Strange indeed.  We'll take a look at it.  Thanks for reporting it...  AndrewGNF (talk) 20:39, 20 November 2007 (UTC)
thread_title:  Any bugs? 

message: Can your bot download images of all PDB files in the Protein Box to the Wikimedia? Then one can easily replace the image in a protein box or include several images (e.g. different domains or different quaternary complexes) whenever necessary.Biophys 02:43, 6 November 2007 (UTC)
replies: text: If we do that we should include a gallery at the bottom of each page so the options are available in wikimiedia are clear to the users that come after the bot. David D. (Talk) 04:00, 6 November 2007 (UTC)
replies: text: We might use a small icon for each PDB structure and allow some brief legend for a group of icons, such as "NMR models of PH domain of 'protein X': 1abv, 2dcf, 4fds". To explain why having many images is so important, please compare this  and this  structures of "the same" protein (one of articles recently created by the bot).Biophys 04:26, 6 November 2007 (UTC)
replies: text: Something like that would be useful for any potential user who wanted to expand the article. David D. (Talk) 04:52, 6 November 2007 (UTC)
replies: text: Right, it is exactly what I am talking about. If the relevant images were already in Wikimedia (and we do not need anything else!), a wikipedian who wants to improve the articles (like me) could easily select the pictures of all domains and quaternary complexes that are needed for each protein and include them in a series of articles. But this user does not have enough time to download many images himself to Wikimedia. That is why we need the bot. Of course, one could download all 15,000 protein images from the PDB to Wikimedia, and that would work even better, or one could make a special "protein image download tool" for that purpose.Biophys 05:04, 6 November 2007 (UTC)
replies: text: I like this idea a lot.  In fact, I just added it as the top priority on the PBB/Ideas page.  However, this task might actually be well suited to a second bot.  It's a nice discrete unit of work that really doesn't need to be integrated into PBB (and yet PBB could benefit from the fruits of the second bot's labor).  Delegating this to a second bot would also help counteract "bloat" in the PBB functionality, and bloat often dooms programs as far as maintainability and future extensibility.  So, anyone have access to some enterprising young undergraduate or graduate student?  David D.?  Or should we try posting at Wikipedia:Bot_requests? AndrewGNF 17:33, 6 November 2007 (UTC)
replies: text: I don't know one off hand I'm afraid. David D. (Talk) 19:38, 6 November 2007 (UTC)
thread_title:  A suggestion 

message: The titles of protein images should be taken as titles of the corresponding PDB files, not as names of proteins. Otherwise, almost all titles are misleading, since the structures do not represent the protein but an isolated domain of the protein or a complex with another protein.Biophys 05:46, 7 November 2007 (UTC)
replies: text: If we follow the same logic of the old protein box, the title refers to the entire box, and then should be the name of the protein. I think that will be better to use the source field as "caption" like in the old template, where you can put "XY domain of protein Z (source:PDB link)" or "Z protein complexed with X" and so on (see here for an example). But I find the bold text in the current template a little too strong for a long caption... the best will be a plain font and small size. Hopefully, this is not a big change, if we decide to do it.--Banus 09:04, 7 November 2007 (UTC)
replies: text: I definitely agree with Banus that the title refers to the entire box, not to the image.  The image caption appears below the PDB image, and by default says something like "PDB rendering based on 2acm".  (As suggested before, I have it on the to-do list to change that caption so that it comes directly from the PDB entry title.)  Accordingly, I'm going to undo your previous edit of MUC1, okay?  Banus, not sure what you're referring to by the "bold text in the current template", but if you have a change you'd like to make, go for it.  AndrewGNF 17:05, 7 November 2007 (UTC)
replies: text: O'K, that is title for the whole protein. But the protein is 1250 residues long, whereas a domain (the image) is only 50-100 residues. Then we need a separate title for the picture, exactly as you said. Otherwise, the image will mislead a reader. The box includes the following text below the picture: "Image source: PDB rendering based on 2acm"  Would it be O'K to replace this text by a title of the picture which would include the name of PDB file (2acm)? "Image source: PDB rendering" is not informative any way.18:20, 7 November 2007 (UTC)
replies: text: Yup, replace that text however you see fit.  (Note though that if you turn off the infobox updating, you won't get updates as far as GO categories, genome locations on new assemblies, and additions to PBB.  Just food for thought -- I still trust humans to make the appropriate choice for their gene(s) of interest.)  If the changes are something generic that we can codify, then we can modify the bot to do it for all bots.  Of course, the best way to up the priority for feature changes is to create a prototype we can reference, so let me know if you do (or just add a link next to the entry on User:ProteinBoxBot/Ideas). AndrewGNF 19:19, 7 November 2007 (UTC)
replies: text: So, the bot would overwrite the image legend during the next update? Then, one might wish to make protein image(s) with their legend independent on the rest of the box to allow the manual modifications and updates.Biophys 20:10, 7 November 2007 (UTC)
replies: text: Yes, as it stands now, any changes in the infobox will get overwritten on the next run.  While we could starting thinking about better ways of handling the infobox content (having a specific update_image tag in PBB_Controls, for example), I think some of the other suggestions you raised have a better cost/benefit.  Two possible intermediate work-arounds.  1) you could keep the update flag as "yes", and when the PBB update stomps your edits on its infrequent updates, you could revert or merge those changes as appropriate.  2) you could add additional images outside of the infobox (or perhaps a new "protein structure" infobox that goes along the bottom of the page?) and PBB won't touch those.  AndrewGNF 21:03, 7 November 2007 (UTC)
thread_title:  Titles of protein images 

message: I suggest using new "Category: Human proteins" instead of simply "Proteins" in the generated articles, and also "Category: Gene from chromosome N". Could you make that?Biophys 18:32, 7 November 2007 (UTC)
replies: text: Yet another good idea.  Added it to the ideas page... AndrewGNF 19:19, 7 November 2007 (UTC)
replies: text:  Just saw that you were proposing a new category for human proteins, which presumably would be a subcategory of Category:Proteins.  Is there a place where we get consensus on a change like that?  I can imagine the powers that be wanting to put some reality checks on new categories (though in this case I'd support the new addition).  AndrewGNF 01:45, 8 November 2007 (UTC)
replies: text: This is trivial. I just created :Category:Proteins by species and :Category:Human proteins. If people do not like it, this can be changed.Biophys 02:05, 8 November 2007 (UTC)
replies: text: Super, I just changed the template to use that category.  I assume it will start populating the new category when some cache expires... AndrewGNF 02:11, 8 November 2007 (UTC)

text: Adding genes in Category:Genes on chromosome N is also fairly simple: copying from Template:Protein you can add  to Template:GNF Ortholog box. Saving strange behaviors in nested templates, the trick should work. The categories "Genes on chromosome N" already exist and will be populated.--Banus 21:55, 14 November 2007 (UTC)
replies: text: Brilliant, I like it...  Done...  AndrewGNF 22:19, 14 November 2007 (UTC)
thread_title:  Categories 

message: So, how many human genes have at least a couple of references in Entrez Gene? One-two thousand? If I understand correctly, you are not going to create articles about any other genes?Biophys 00:41, 8 November 2007 (UTC)
replies: text: According to the Oct 30 2007 release of the gene2pubmed file, there are 25694 unique human entrez genes.  Of those, 20078 have at least 2 linked pubmeds, 17305 have at least 3 linked pubmeds, and 15380 have at least 4 linked pubmeds.  Note though that many of those linked pubmeds are huge genome-wide studies.  Take, for example,  and  which are associated to 18009 and 11328 human genes, respectively.  So I don't know that the # of linked pubmeds is the right thing to draw a threshold on.  Personally, I don't think there's a need to draw a strict and hard threshold.  We'll stop when they stop being uniformly useful.  From there, we'll add only on the basis of specific requests (or a consensus that we should keep going).  AndrewGNF 01:51, 8 November 2007 (UTC)

text: Thank you for explanation. References to genome-wide studies would not qualify. Biophys 06:04, 8 November 2007 (UTC)
thread_title:  Scope of the project 

message: It seems that you just included Gene ontology in the Protein Box. This is something which requires third opinion and community discussion. It makes the Protein box very big. If I understand correctly, Gene ontology is a low-quality computer-generated annotation, unlike curated Entrez Gene abstracts and UniProt records. I would not recommend this as a part of Protein Box, but rather as additional links or another box at the bottom of the article.Biophys 06:04, 8 November 2007 (UTC)
replies: text: Yes, I'm open to further discussion of this topic, but please remember that this bot has undergone extensive "community discussion" in many forums prior to approval, including on this talk page, in WP:MCB/Proposals, and on the bot approval page.  Our primary goal right now is to execute the consensus plan that was decided on during those discussions.  Gene Ontology functional annotations come from a variety of sources.  Check out the Entrez Gene page for BTK and scroll down to the Gene Ontology section.  To the right side of the table, each annotation is provided with a three-letter code that indicates the source of the annotation.  The three letter codes can be decoded here.  I believe one-click access (through the Entrez Gene link) is the appropriate level of accessibility to this information (integrating it directly would clutter and obfuscate). AndrewGNF 16:56, 8 November 2007 (UTC)
replies: text: Sorry, I was not clear. I think that "hidden" link to Gene Ontology is great (as it is in TOP2B right now - with small "show" icon to the right). I just did not like when the Gene Ontology menu was always open for some reason yesterday, which made the protein box too big.Biophys 18:25, 8 November 2007 (UTC)
thread_title:  Gene ontology 

message: This is just something to think about. Entrez Gene has a well-defined Table of interaction partners for each human protein - with supporting references. All these partners are other human proteins, whose articles will be included in WP as a result of this project. Hence each interaction partner has (or will have) an internal link in WP. Therefore, WP is uniquely equipted to deal with protein-protein interaction networks. It would make a lot of sense to create a Table of human protein interaction partners in each article about a human protein - automatically by this bot. That would also be encyclopedic since each partner/interaction is supported by a reliable source. For example, 
:Interaction partners of CUL1: 
:SKP2 (reference), (comment), 
:RAC2 (reference), (comment),
:RBX1 (reference) and so on.Biophys 15:16, 9 November 2007 (UTC)
replies: text: Another excellent idea...  And I agree, the synergy between protein interactions and wikilinking make this very attractive...  AndrewGNF 16:53, 9 November 2007 (UTC)
thread_title:  Interaction partners 

message: This 'bot is creating lots for strange articles that will truly mess up searches. Most people who search for "sumo" won't be looking for SUMO2. I would prefer that these articles' titles were prefixed with the string "Human Gene"; e.g. I would have the bot create a Human Gene SUMO2 article.--Mumia-w-18 02:25, 10 November 2007 (UTC)
replies: text: Search seems fine to me...  AndrewGNF 02:30, 10 November 2007 (UTC)

text: What in specific are you referring to?  I think most biologists would think that these stubs are good starting places for encyclopedia articles.  Check out relevant discussions here and here. AndrewGNF 02:33, 10 November 2007 (UTC)
replies: text: I read those pages, and I'm not impressed by the lack of discussion about who is going to maintain and protect those pages. My concerns are in the section titled "ProteinBoxBot objections."--Mumia-w-18 04:26, 10 November 2007 (UTC)
thread_title:  Better names for gene articles 

message: Coming across these articles in new pages patrol, I considered blocking the bot while we discuss the fact that as Tim Vickers noted at the end of the previous section, consensus was that "these articles must contain reliable sources". The bot is not implementing that decision and is creating many unsourced articles. I do not know exactly how many as I would need a bot to check them all. Some of the articles created have further reading sections. Being referred to an outside source for further study is not the same as providing a reference to a source verifying the information in the article. 
A quick perusal of the last 50 articles created reveals 8 articles with only "further reading" sections: SLC9A3; SLC37A4; SLC15A1; RUVBL1; PPP5C; RAPGEF3; CD83 and NONO; and 8 articles with no even putative references: SAA2; ARAF; ETV4; DLG3; RCC1; CUL4A; PIAS4; and PPP1CC. That's sixteen out of 50 articles or 32%. 
Considering the possibility that the bot may do a second pass for whatever reason, so looking at the most recent fifty might be deceptive, I went back to earlier articles created and the first one I clicked on at random, CRY1, was unreferenced. I don't know if this is a malfunction or not strict adherence to the criteria established, but it should stop and the articles created without references should be remedied by the bot or programmed to be tagged with . I refained from blocking since this is done in small batches so there should be an opportunity of discussion before massive numbers of new articles are created. 
A second issue of concern is that though there is no prohibition on locally uploading free license images, our policy pages strongly encourage that free images to be uploaded to commons. I don't think it's a good idea to have this bot uploading thousands of images locally. I understand, of course, that there is likely a whole separate bot approval process at the commons, but that doesn't mean that we should forego what is proper because more hoops must be jumped through.--Fuhghettaboutit 15:07, 10 November 2007 (UTC)
replies: text: I have just noted that some of the infoboxes contain links to  sources. That's better than nothing but is still no substitute for a transparent, flagged source in the article proper.--Fuhghettaboutit 15:22, 10 November 2007 (UTC)
replies: text: I agree with Tim. Besides, I have seen a lot of WP articles without any sources. The Protein Box bot could simple tag such articles as "unsourced" for further improvement by the people and the next generation of the bot. There is no serious reason for stopping the bot.Biophys 18:09, 10 November 2007 (UTC)

text: Please also see WP:Source. It says: "A reliable source is a published work regarded as trustworthy or authoritative in relation to the subject at hand." Hence the links to established scientific databases qualify as references to reliable sources.Biophys 18:18, 10 November 2007 (UTC)
replies: text: First, I'm not sure what you are agreeing to but you don't seem to be echoing what Tim said. The fact that you have seen a lot of unsourced articles on Wikipedia is the problem. In fact it's a cancer on Wikipedia, and is no proper rationale for allowing a process to create more. Please see WP:OTHERSTUFFEXISTS. Second, your citation to what constitutes a reliable source is inapposite to whether that source is referenced. I am not disputing the reliability of any sources. The problem at issue is that there are a large percentage of these articles that are not showing any source as a reference if my statistical sampling of the last 50 created was at all reliable. If what you are looking for is a statement in policy that placing a link in an infobox is analogous to creating a references section with citations populated, you won't find it and for good reason. I also agree with Tim—this should be worked out first.--Fuhghettaboutit 18:52, 10 November 2007 (UTC)

text: I agree with Fuhghettaboutit. The 'bot should be disabled while it's being fixed. And while the sources for CRY1 may be reliable, there are still no references. Nonetheless, even if I consider the links to be adequate replacements for references, I still cannot get the data. Please click on the CRY1 link in this article.--Mumia-w-18 18:38, 10 November 2007 (UTC)

text: I should clarify that I get this response from Mozilla Firefox when I click that link: "Firefox can't establish a connection to the server at www.gene.ucl.ac.uk."--Mumia-w-18 18:40, 10 November 2007 (UTC)

text: I think this is just a malfunction though, the references exist but for some reason they weren't added to the stubs by the bot. Tim Vickers 18:33, 10 November 2007 (UTC)
replies: text: I wonder if that is the reason why it malfunctioned? Does the bot have external dependencies? Tim Vickers 18:44, 10 November 2007 (UTC)
replies: text: It's not a malfunction per se.  We, the wikipedia community, decided (on one of those discussion pages) that we would limit references to review articles only.  Other users raised concerns about too many references listed...  Anyway, the bot was approved with that protocol in mind, but since multiple experienced editors are chiming in here, we'd be open to discussing this spec again.  New proposal: link all review articles, and if less than 10, add primary articles up to 10.  Sound good?  If anyone has an issue with this revision, please raise it by Monday.  Changing code and specifications at this point is non-trivial, so I'd like to minimize them before the first-pass run is complete.  AndrewGNF 18:50, 10 November 2007 (UTC)
replies: text:  HGNC link fixed.  AndrewGNF 18:54, 10 November 2007 (UTC)
replies: text: If I understand you, you're talking about listing ten separate  sources now? I'm not overly concerned that there be a wealth of sources when the information is one sentence. The main issue is that a source or sources be placed in a references section and thus are clearly a reference for the text in the article, rather than a link in the infobox. At best, this should be an inline citation, which provides the markup for future human editors who often don't know how they are created and have no idea where to go to find out.--Fuhghettaboutit 19:08, 10 November 2007 (UTC)

text: I think we have the following problem: (a) there is a huge amount of notable biological subjects to include them to WP as independent articles (almost all human proteins are notable per WP:Notability), and (b) there are too few wikipedians who can do it. That is why we need such bots.Biophys 00:48, 11 November 2007 (UTC)

text: Do you have a list of drawbacks? David D. (Talk) 09:10, 11 November 2007 (UTC)
replies: text: I asked an opinion of my friend who is very skeptical about everything. He said: "This work does not make any sense because the articles created by the bot are not better than the original biological database(s).  In fact, the original databases are better and more useful because they provide links to the protein interaction partners and other information missing in the created stubs". Of course, we are not going to compete here with professional biological databases,  and we work to create a very different educational resource... However we do not really know if this project will really work in WP environment. If few people work with created stubs, this project might be of little significance. Let's try and see.Biophys 05:29, 12 November 2007 (UTC)
replies: text: Maybe your friend does not understand the goal.  These are seed articles.  There is no intention to add more than the databases themselves already have. Once these articles are in place they will start to be linked to from other articles.  Other users will add to the articles and some will grow (maybe many will grow).  Researchers will come and improve their favourite genes.  I suspect this would never happen without the seed.  Worst case scenario is they all sit there unedited for the next ten years. If so, no real problem. I doubt this will be the case and in fact we might see a massive influx of editors due to this initiative. David D. (Talk) 05:37, 12 November 2007 (UTC)

text: Whew!  Who knew so many people were watching this thread!  After Fuhghettaboutit pointed it out, I agree that the commons is definitely something that we should look at.  I've accordingly added it to our ideas page for version 2.  However, since this is not an official policy (only a recommendation), and since the bot was approved with the images clearly hosted at WP, I am reluctant to further delay implementing the approved "Version 1" plan.  Remember the dot, if this is reasonable to you, please log your support below.  (If not, please come back when we're drafting specs for version 2... ;) )  AndrewGNF 23:58, 13 November 2007 (UTC)
thread_title:  Unreferenced articles are being created and apparently in large numbers 

message: Well, haven't yet heard back from Fuhghettaboutit, but I'm going to hope that the two more recent signers in the support column are enough to keep moving forward.  We've started PBB back up on creating pages.  Of course we're still open to further discussion on how to fine tune things, but sounds like the effort as a whole is still sound.  So, while we sort out the details, we're moving forward with page creation, both in a fully automated manner (when there are no namespace conflicts) and in a semi-automated manner (with our small but effective team of volunteers).  Implementing changes later will be pretty easy -- the hard part is getting the page in the right location in the first place.  AndrewGNF 21:48, 14 November 2007 (UTC)
thread_title:  Moving forward 

message: Is it intended that the bot removes links from the article it is editing? For example, it removed all links from CASP6 and added a bunch of references, most of them not really necessary in this article. — Tirkfltalk 08:39, 15 November 2007 (UTC)
replies: text: The bot copies the text from Entrez Gene whenever it update. When you change the text, you need to change the bot controls in order to preserve it. See here for an example. --Banus 12:16, 15 November 2007 (UTC)
replies: text: Yeah, unfortunately, there is no easy way to preserve the links created in the summary on a bot over-write.  While it may be possible to spend a few days building code to preserve links on an overwrite, that would be something for version 2 of the bot.  I'm going to leave a note about the nature of such an algorithm here:  It would be a complicated text parser that compared the current text to the new text - where the text was the same, but one had a wikilink, it would then add the wikilink to the new text.  It could also log all the words that are currently wikilinked, and then wikilink the same words that appear in the new text.  Definitely something we are not going to code up now (due to lack of time mainly), but that could be done in the future. Sorry for the current inconvenience.  This shouldn't come up very often at all right now as we are just trying to generate/merge new pages and not update pages (though a large batch of pages must be redone at this point...)  JonSDSUGrad 20:02, 15 November 2007 (UTC)
replies: text: And just to emphasize, the solution for now is to disable the summary updates completely (as shown in the link posted by Banus above).  Entrez Gene doesn't update those summaries often/substantially, so I'd much rather have even one human-added wikilink than the absolute latest and greatest summary from Entrez Gene.  I try to look at all the diffs for PBB updates (or watching for wikilinks in the summary) so I can disable the flag, but I missed this one.  If anyone else notice either of these cases in genes they watch, please feel free to change the PBB flag accordingly...  AndrewGNF 20:13, 15 November 2007 (UTC)

text: You could reduce the problem by comparing the Entrez summary text to the log of the last run and only updating the page if the Entrez database has changed. Tim Vickers 20:05, 15 November 2007 (UTC)
replies: text: Yeah, we thought a bit about solutions like that.  But that would require logging a history of Entrez Gene summaries and I think that might be a lot of work too.  We can discuss options over V2 specs though.  Personally, I favor the disabling of the summary updates as the long-term solution.  After all, it's my great hope that eventually, these summaries from Entrez Gene will be obsolete, replaced by more current and more dynamic summaries written by wikipedians... AndrewGNF 20:17, 15 November 2007 (UTC)
replies: text: This is not a problem if an editor knows that summary update should be turned off by writing "no". What should be done ASAP is decoupling of protein images (PDB structures) and other content of the ProteinBox, because turning ProteinBox updates off is not advisable, and therefore one can not correct the titles of protein structures (which are not informative at best) or replace protein images, as I noted above.Biophys 20:36, 15 November 2007 (UTC)
replies: text: My apologies, I was wrong about this.  Straight from JonSDSUGrad, "It does not overwrite those two fields - any changes will persist through an update.  The only time that PBB updates those fields is when no information is present in them."  That's the problem when PBB's mouth is decoupled from PBB's hands... ;)  So, edit/update the PDB fields as you see fit while leaving the update flag as "yes". AndrewGNF 20:51, 15 November 2007 (UTC)
replies: text: Thank you! This is really great, except that links to PDB files are not regularly updated (a lot of new structures are deposited to PDB every month).   An ideal solution would be to update automatically the list of PDB files in the ProteinBox but allow user to select one or several of them for the image and make himself the title for the image(s). Of course, it would be fantastic to have an automated  "downloader" of images from the PDB to Wikimedia, which is basically one of the bot's subroutines. I do not know if the present version of the Bot allows a user to specify himself one or several PDB structures for the image(s).Biophys 22:48, 15 November 2007 (UTC)

text: Just to clarify, there are three parameters in the infobox that may be relevant.  "image" indicates which image is actually displayed at the top of the infobox.  "image_source" spells out the caption for the image.  "PDB" lists all known linked PDB images and is shown by "Available structures" label in the rendered page.  The first two (image and image_source) are skipped by PBB if there are already values there.  The PDB field will be updated unless the update is turned off in the control template.  So, newly submitted PDB structures will appear as additions on subsequent runs of PBB. AndrewGNF 23:03, 15 November 2007 (UTC)
replies: text: Great! So everything is perfect. Easy downloading of additional PDB images is certainly a separate question which should not be addressed right now.Biophys 02:33, 16 November 2007 (UTC)
thread_title:  Bot is removing links 

message: Will Jon's source code be placed in a public depository (i.e., SourceForge.net or something like it)? --Arcadian (talk) 01:06, 17 November 2007 (UTC)
replies: text: Absolutely.  I think he's a little bashful about it right now because of how many twists and turns I (we) threw at him -- it's gotta look like spaghetti code.  But he's not getting his degree until it's posted somewhere... ;) AndrewGNF (talk) 03:16, 17 November 2007 (UTC)
thread_title:  Source code 

message: It is really important to categorize the proteins as say "GPCR", "ABC transporters", etc. Your company database has InterPro family fields. Is any way to include the InterPro links anywhere, which would significantly facilitate the categorization?Biophys (talk) 06:40, 17 November 2007 (UTC)
replies: text: Yeah, we know InterPro is important, but it was a question of priorities.  For whatever reason, during V1 spec determination, it didn't make it into the final specs.  And just because it's in our database, doesn't mean it's simple to incorporate into PBB in a timely manner.  I know it's not terribly satisfying, but all I can say is we'll get it in Version 2.  AndrewGNF (talk) 19:28, 17 November 2007 (UTC)
replies: text: I agree. There is nothing urgent here. Let's wait for version 2.0 and then make the categories.Biophys (talk) 21:06, 17 November 2007 (UTC)
thread_title:  Protein families and categories 

message: I realize you're probably getting tired of all these code tweaks, but I was editing Apolipoprotein H and came across a "feature".  I liked the image that was in the protein box previously and incorporated it into the new protein box.  However, when I also incorporated the caption it ended up saying:  "Image source: Apolipoprotein H showing positively (blue) and negatively (red) charged regions."  Forluvoft (talk) 18:48, 17 November 2007 (UTC)
replies: text: I guess on the image's WikiMedia page, it lists the original PDB file.  I can throw that in so it makes sense.  Forluvoft (talk) 19:02, 17 November 2007 (UTC)
replies: text: Well, I actually prefer keeping the original caption as well, especially when it gives more information than just the PDB code.  Do you have a suggestion as to how to handle it?  I actually don't think it's too confusing with the "Image source" tag in there, but we could also just remove the caption label altogether.  (Easy change of the template.)  AndrewGNF (talk) 19:33, 17 November 2007 (UTC)
replies: text: I would vote for just getting rid of "Image source."  It's probably not even necessary for a default PBB caption such as " PDB rendering based on 1cmo."  But again, this isn't really a major issue.  Forluvoft (talk) 20:36, 17 November 2007 (UTC)
replies: text: I agree with Forluvoft. The title like "Image source: PDB rendering based on 1a25" in PRKCB1 does not make sense. One could simply make title: "Image of PDB entry 1a25". A good and correct title would be one from the TITLE field of the PDB file, which is "C2 DOMAIN FROM PROTEIN KINASE C (BETA)". Indeed, this is not image of Protein kinase C (as a reader would think from the titles generated by bot); this is image of C2 domain.Biophys (talk) 20:59, 17 November 2007 (UTC)

text: Simple solution of changing the template is done.  Look good for now?  (Again, to refresh the cache for a gene page, hit edit then save...)  Biophys, your idea to get the caption from the PDB title is already on the Ideas page...  V2... AndrewGNF (talk) 21:13, 17 November 2007 (UTC)
replies: text: Thanks!  :)   Forluvoft (talk) 22:19, 17 November 2007 (UTC)
thread_title:  "Image source" in caption of protein box 

message: :: I'm happy to do requests.  If you have a group of genes you would like to have run, just get me a list of Entrez Gene Ids and I'll be happy to put it in the queue. JonSDSUGrad (talk) 19:27, 22 November 2007 (UTC)
replies: text: Thank you! But the list of human single-pass proteins would be at least 2000  long (this project is mostly about protein/peptide structure modeling and some bioinformatics, rather than studies of a few specific proteins). I could try however to automatically generate some WP-formatted content about these proteins in my namespace (a content to be merged with existing or future articles). Ironically, that would mostly be a content which PBB 1.0 is missing: protein family, domain structure, subcellular localization and function - everything is encyclopedic...Biophys (talk) 18:09, 23 November 2007 (UTC)
replies: text:  I just figured out a way to generate lists of Entrez IDs given the Gene Symbol.  On the Entrez FTP site is a flat file called DATA/gene_info.gz which contains one gene per line and each line contains the Entrez ID + Gene name + other info.  One can simply grep to find the gene, and therefore the Entrez ID that you are searching for.  Based on data extracted from this file, I just created a table for the voltage gated ion channels.  Cheers.  Boghog2 (talk) 21:40, 23 November 2007 (UTC)
replies: text: Good to know that! I am thinking however, would it be reasonable to do the following. 1. To create automatically a single file with information on several hundred of proteins or protein families using Pfam/Entrez/Uniprot files as input and formatting everything exactly as needed for a series of WP articles (my programming skills are sufficient to do that). The file would be basically a sequence of articles (or some content missed by PBB and organized by articles): article 1, article 2, and so on. 2. Quickly merge the file's content to existing or/and new WP aricles using AWB? Biophys (talk) 23:38, 23 November 2007 (UTC)
replies: text: Since we have that resource, could/should we create a page with wikilinks to the gene name for the list of pages intended to be created by the bot? Then, if you grepped on the raw HTML on the Wikipedia page, you can identify which links are red (therefore, no namespace conflict), which could help address Andrew's concern above.  --Arcadian (talk) 01:50, 24 November 2007 (UTC)
replies: text: Good idea.  As a start, I have added the WP links to the gene names for three protein familes (voltage-gated ion channels, ligand gated ion channels, and solute carrier family) here.  As I have stated elsewhere, I think it would be a good idea if possible to process each of the major gene/protein families one at a time so that all the members of a particular family are added at the same time.  This will make integrating with existing WP content easier. Boghog2 (talk) 10:09, 24 November 2007 (UTC)
replies: text: I have now also added lists of transcription factors and the six Enzyme classes (EC1-6) here.  I have forward a list of GPCR genesymbols/Entrez ID to Andrew previously.  With more work, we could probably produce list for the other major families.  Boghog2 (talk) 17:40, 24 November 2007 (UTC)
replies: text: Right. It makes so much sense to include all proteins/genes family by family and do not forget to include the name of each family as a category (e.g.:Category:Ligand gated ion channels) in the corresponding pages.Biophys (talk) 01:40, 25 November 2007 (UTC)

text: My last comment was directed to Boghog's statement, but appeared below, due to simultaneous editing. However, I support Biophys's proposal. Here is a list of pages using the existing protein box. --Arcadian (talk) 01:54, 24 November 2007 (UTC)
replies: text: We had a discussion with Boghog on a related topic here. I will try to generate a few examples in my namespace, as time allows, and then ask for everyone's opinion.Biophys (talk) 02:26, 24 November 2007 (UTC)

text: Oops, these people found 3,853 human protein Pfam-A families .Biophys (talk) 23:46, 28 November 2007 (UTC)
thread_title:  Protein families 

message: P.S. I do not know if you realize this, but each UniProt entry is a variety of a ProteinBox. However, "Uniprot ProteinBox" includes some important information missing in our Protein Box. For example, :
:FUNCTION: Occurs in almost all aerobically respiring organisms and serves to protect cells from the toxic effects of hydrogen peroxide. 
:CATALYTIC ACTIVITY: 2 H2O2 = O2 + 2 H2O. 
:COFACTOR: Heme group. 
:COFACTOR: NADP. 
:SUBUNIT: Homotetramer. 
:SUBCELLULAR LOCATION: Peroxisome. 
:DISEASE: Defects in CAT are the cause of acatalasia [MIM:115500]; also known as acatalasemia. This disease is characterized by absence of catalase activity in red cells and is often associated with ulcerating oral lesions. 
:SIMILARITY: Belongs to the catalase family. Biophys (talk) 02:39, 24 November 2007 (UTC)
replies: text:  I agree that the above information would be very useful to include, but one first must look at the UniProt terms which in turn applies the Creative Commons - No Derivative Works license which states "You may not alter, transform, or build upon this work."  I don't know if I am interpreting the UniProt terms correctly, but it would appear that incorporating UniProt derived data into WP would constitute "transforming" the work and hence would not be permitted under the UniProt terms.  At a minimum, I think we would have to obtain permission from UniProt before even considering such an undertaking.  Cheers. Boghog2 (talk) 08:40, 24 November 2007 (UTC)
replies: text: Right. I left the copyright question to Alex Bateman. We need to ask a UniProt permission, and it is probably important who would ask.Biophys (talk) 23:06, 24 November 2007 (UTC)
replies: text: You should see more complete explanation however: . The biological data in databases are not protected by copyright.  It tells: "whether the data itself is copyrightable, depends on what it is. To the extent it consists of factual information, it will not be copyrightable. For example, the contents of NCBI’s Entrez Gene database include gene names, descriptions, pathways, protein products, and other facts. However, to the extent the data is creative and expressive works, such as papers or photographs, then the database content itself is likely to be protected by copyright." Hence aa sequences, locations of protein domains, assignemt to a certain protein family; oligomeric state, catalytic activity, subcellular location, or biologiacl function themselves are not protected by copyright, although the entire Table can be protected because it includes some creative elements, such as names of database fields and overall organization of data. As for summaries by database annotators - this is not quite clear. If they qualify as "creative essay", they are protected. If they are simply "data", they are not protected.Biophys (talk) 22:35, 25 November 2007 (UTC)
thread_title:  UniProt entries 

message: I've created a template called Template:NLM content that can be put on Main–namespace pages to show that a page's text was copied directly from the NLM. Use it if you'd like. — Insanity Incarnate 09:22, 22 November 2007 (UTC)
replies: text: Awesome!  Thanks for this.  I'll have to check and see if we can make use of it. JonSDSUGrad (talk) 19:15, 22 November 2007 (UTC)

text: So, the articles now have the following text at the bottom: "This article incorporates text from the United States National Library of Medicine, which is in the public domain.". Sorry, but I think this text should be deleted as misleading. As soon as any wikipedian makes a single edit in the Abstract (which suppose to be the case for every article), this is not a text from the United States National Library of Medicine any more.Biophys (talk) 19:05, 26 November 2007 (UTC)
replies: text: I think the acknowledgment/disclaimer text is necessary and important and therefore should be included by default.  If the article is later substantially edited so that the original text is replaced, then the template can be deleted, but only after significant editing.  I have had at least one bot and two administrators issue warning to me after I manually added some PBB generated content.  I am now including this disclaimer on all pages that I create that incorporates any NLM text.  Boghog2 (talk) 19:14, 26 November 2007 (UTC)
replies: text: I see. You have notified already User:Coren (but there is also User:Where - User:Wherebot) who operate such bots, so he will include the NLM address to the list of websites which content can be freely copied to WP (he suppose to have such list(s)). There is already a citation of Entrez Gene database, so the NLM template is a duplicate acknowledgement and an additional link to delete for anyone who will edit an article in the future. But I do not care. Let's have this template - no problem.Biophys (talk) 23:15, 26 November 2007 (UTC)
replies: text: Perhaps Template:Gray's would be a good model: "This article was originally based on an entry from a public domain edition of Gray's Anatomy. As such, some of the information contained herein may be outdated. Please edit the article if this is the case, and feel free to remove this notice when it is no longer relevant." --Arcadian (talk) 02:57, 27 November 2007 (UTC)
replies: text: I agree. That would be better.Biophys (talk) 06:56, 27 November 2007 (UTC)

text: How about adding something like "Feel free to remove this template after editing if it is no longer true." — Insanity Incarnate 21:12, 28 November 2007 (UTC)
replies: text: Same thing but shorter.Biophys (talk) 17:13, 29 November 2007 (UTC)
thread_title:  New template 

message: What is the point of creating stubs for genes if nothing is said about what they do? For example, GPR155, GPR156, GPR157, GPR158 all read exactly the same. Aren't you just mirroring some database(s)? Adding 10,000 stubs will increase the size of Wikipedia by 0.47%. AnteaterZot (talk) 08:59, 12 December 2007 (UTC)
replies: text: Those GPCR genes were created by request -- see User_talk:ProteinBoxBot.  Presumably now that those stubs are created, the interested user(s) will add additional useful content.  But, I'd argue that the stubs even as they are now are useful and notable (also the consensus of the BAG, MCB, etc.), even if slightly less full than some of the other gene pages.  AndrewGNF (talk) 17:34, 12 December 2007 (UTC)
replies: text: So you are not planning on creating 10,000 such stubs? AnteaterZot (talk) 23:32, 12 December 2007 (UTC)
replies: text: Yes, we eventually will work up to ~10k genes, as described on the bot approval page.  Not sure what you're getting at here... AndrewGNF (talk) 00:03, 13 December 2007 (UTC)
replies: text: What I'm getting at is that most of the genes in the world are not notable. For example, fruitless is notable. AnteaterZot (talk) 00:08, 13 December 2007 (UTC)
replies: text: Well, the notability issue has been discussed extensively on the bot approval page, on the MCB/Proposals page, PBB talk page, and at the village pump.  (Sorry, if you can't find any of those pages, I'm happy to wikilink.  Just feeling lazy...)  Each time, the consensus of users has been to move ahead.  If you still want to raise notability issues (hopefully with arguments that haven't been previously raised), I'd suggest doing it at the bot talk page.  AndrewGNF (talk) 00:13, 13 December 2007 (UTC)
replies: text: Well, okay. And I think it would be very kind of you to provide maybe one link that would lead me to the others. AnteaterZot (talk) 00:17, 13 December 2007 (UTC)
replies: text: Done, added two links... AndrewGNF (talk) 00:20, 13 December 2007 (UTC)
replies: text: I've looked it over, and I must commend you in your efforts to digest material from the various databases into a more accessible format than Entrez. But a couple of things still worry me. One is the assertion that a gene is inherently notable; "Notability of the genes themselves, I think, is a given. These are human genes, the stuff of life!" This is simply not true. Most genes, if knocked out, have little or no effect on phenotype. You address this by requiring the gene be mentioned in more than a couple papers, which is a good start. Two is the heavy reliance on primary sources, and I mean this in the scientific literature sense. Wikipedia requires secondary and/or tertiary sources to establish notability. I take this to mean that a gene should have a couple of mentions in review articles, and/or a mention in the popular press. Take for example, BRCA1. It has 174 mentions in the New York Times. You might say that example is a bit unfair, so how about C5a receptor? It appears in the title of a couple of review journals, and here in a story about a pricy biotech startup. So it might be okay. Now let's take one your bot created, GPR32. It has 208 unique g-hits, none of which amount to anything. I found only one citation on webofknowledge, the (Marchese et al. 1998) one, which is a short communication. They don't really seem to know what the gene does. The gene does not appear to have been in the title or abstract of any review articles. Therefore the gene appears to be not notable. Do you disagree? AnteaterZot (talk) 10:56, 13 December 2007 (UTC)

text: Having said that, is there any way you can tune your bot to not create stubs on genes like GPR32 while keeping notable ones? Perhaps it can require the word "review" in two sources? AnteaterZot (talk) 10:56, 13 December 2007 (UTC)
replies: text: I second Andrew's suggestion to move this discussion to the PBB talk page.  Since I was the one that requested these GPR pages, I feel that I have an obligation to respond, but on the PBB talk page, not here. Cheers Boghog2 (talk) 17:20, 13 December 2007 (UTC)
replies: text: So moved. Is the bot active? AnteaterZot (talk) 23:47, 13 December 2007 (UTC)
replies: text: No, it is not active for a couple of weeks.Biophys (talk) 00:16, 14 December 2007 (UTC)

text: The idea that "Wikipedia requires secondary and/or tertiary sources to establish notability." is true, but the definition of "secondary" here encompasses articles in peer-reviewed journals. The guideline states "A topic is presumed to be notable if it has received significant coverage in reliable sources that are independent of the subject." A gene that is the subject of even one paper might meet the notability guideline, those that are the subject of multiple papers certainly meet the guideline and those that are the subject of review articles (tertiary sources) are indisputably notable. Tim Vickers (talk) 00:04, 14 December 2007 (UTC)
replies: text: So, do you claim that GPR32 is notable?  When policy says "sources", it means more than one source.  If a gene, say, caused people to have three eyes but was only in one paper, it would be notable.  But most genes are not notable. AnteaterZot (talk) 00:20, 14 December 2007 (UTC)
replies: text: I would argue that all human genes should be considered notable, based on the notability of the human genome as a whole. To avoid overload, I suggest that the notability of animal and plant genes should be judged individually. Similarly the notability of proteins should be judged individually. Apparently the current thinking at WP:N is that all towns and cities in the world are notable, no matter how small, so long as their existence and naming can be reliably sourced. (See WP:OUTCOMES).  It is not too much of a stretch to allow human genes into the realm of intrinsic notability. (How many things can be more important?)  EdJohnston (talk) 00:39, 14 December 2007 (UTC)
replies: text: Notability is not inherited. See Wikipedia:Arguments_to_avoid_in_deletion_discussions#Notability_is_inherited. AnteaterZot (talk) 00:51, 14 December 2007 (UTC)

text: And, I disagree. As I said before, you could be walking around right now, missing both copies of a gene, and not show any effects. In fact, it is likely that you have at least one non-functional gene. What if I wanted to add a stub for every known SNP to Wikipedia? AnteaterZot (talk) 00:51, 14 December 2007 (UTC)
replies: text: Huh? this a strawman argument, you can't compare SNP's with genes. Also since when has a gene only been notable if it has a phenotype when knocked out? David D. (Talk) 07:29, 14 December 2007 (UTC)

text: Articles created on request are not covered by the ProteinBoxBot notability requirements. We create them and then pass them over to the person who requested them, so they can improve the article themselves. If you want to AfD these examples, go ahead, but this isn't characteristic of the output that the bot is making. Have a look at the pages created in User:ProteinBoxBot/PBB Log Index to get a better idea of the standards we follow. However, I disagree with the idea that all human genes are intrinsically notable since there is no reason to bias this towards humans and the same argument could be applied to any species on the planet. That would be an indiscriminate and uninformative collection of information. Tim Vickers (talk) 00:41, 14 December 2007 (UTC)
replies: text: Could you give me six (completely random chosen) stubs on human genes the bot created without any human request or intervention, so I can check them out? AnteaterZot (talk) 00:51, 14 December 2007 (UTC)

text: Choose an integer between 1 and 65. Tim Vickers (talk) 00:55, 14 December 2007 (UTC)
replies: text: 18 AnteaterZot (talk) 00:56, 14 December 2007 (UTC)

text: From log file 18 on the page I linked above, the bot created/updated SUMO2, STX4, C1S, Thymidine kinase 1 and SLC9A3R2. Tim Vickers (talk) 00:59, 14 December 2007 (UTC)
replies: text: Okay, I'll look at them. It will take me awhile. Can you give me 5 more from log file 19? I think a slightly larger sample would be better. Thanks, AnteaterZot (talk) 01:04, 14 December 2007 (UTC)

text: Here's the page User:ProteinBoxBot/PBB Log Wiki 11-9-2007-A2-4, have a look at the content and referencing. Tim Vickers (talk) 01:08, 14 December 2007 (UTC)
replies: text: May I also suggest ?  (scroll down past all the GPCRs) AndrewGNF (talk) 01:09, 14 December 2007 (UTC)
thread_title:  Discussion on notability moved from AndrewGNF's talkpage 

message: Just a quick question: At random, I chose OPN5.  I then looked for review articles in the reference list, clicked on .  I read the whole article, searching for the gene.  It turns out the gene is only mentioned in one of the citations of the article, but when I looked at what the reference was pointing at, found a very general statement about opsins.  What this means to me is that the bot, not knowing any better, pulled this article from a database as a source, which it really isn't.  So, why not tell the bot to only take sources where the gene name is in the title or abstract only?  Next, I looked at .  This paper doesn't mention the gene at all!  How did that happen?  This is an issue distinct from notability; you don't want the bot using bad citations, right?  Anyway, I'm going to go on with my notability investigation, be back later. AnteaterZot (talk) 04:54, 14 December 2007 (UTC)
replies: text: Well i rechecked this since it seemed surprising that OPN5 would not be mentioned in this review. I counted the neuropsin subfamily mentioned quite a few times. Isn't that synonymous with OPN5? David D. (Talk) 06:41, 14 December 2007 (UTC)

text: When I made a regular PubMed search using "OPN5" as a search word, I got these two references:  and . One of them is indeed about OPN5 gene/protein. Perhaps the selection of references can indeed be improved. Does it means that this gene is not notable? Not at all. The publication (a reliable source) claims that "Neuropsin shares 25-30% amino acid identity with all known opsins, making it the founding member of a new opsin family." That may be notable enough. "A founder" of something would be great if said about a person (just kidding). 05:42, 14 December 2007 (UTC)
replies: text: That's not what that means. AnteaterZot (talk) 05:43, 14 December 2007 (UTC)

text: And no, by WP:N, it is not notable, because more than one source is required and the sources must be secondary or tertiary. The primary sources are good for WP:V. AnteaterZot (talk) 05:54, 14 December 2007 (UTC)
replies: text: If you insist, we would have to discuss if the established biological databases (like UniProt and Entrez) qualify as reliable secondary sources about the genes.  What would be your arguments that they do not?Biophys (talk) 06:02, 14 December 2007 (UTC)
replies: text: In the scientific literature, a secondary source is a review article. Databases are directories, and primary or below (zeroary? halfary?). AnteaterZot (talk) 06:08, 14 December 2007 (UTC)

text: Correct. There are two more sources.Biophys (talk) 06:07, 14 December 2007 (UTC)
replies: text: Okay, up to three primary sources. Without a secondary or tertiary source, the gene is not notable. You could have a dozen primary sources, but if scientists haven't talked about the gene in a review article, it can't be all that important. Compare it to my BRCA1 and C5a receptor examples above. AnteaterZot (talk) 06:13, 14 December 2007 (UTC)
replies: text: Just looking at what cites the primary source leads to . I think the main point is lost here.  These articles are starting points not finished products. David D. (Talk) 06:31, 14 December 2007 (UTC)
replies: text: Guys, in general I think the project of getting these genes onto Wikipedia is great.  I'm not trying to sabotage your plan, just to improve it.  David D. found what looks like a secondary source; great.  "Why didn't the bot list it?" is the question you should be asking yourselves.  AnteaterZot (talk) 06:54, 14 December 2007 (UTC)
replies: text: I didn't mean to sound defensive, these are legitimate questions but these bots are only as good as the data bases they mine.  Part of the problem is there are very many references cited and a subset are grabbed, Andrew will correct me if I'm wrong here. I agree in principle that only taking ones with OPN5 in the title is good but in practice that will not solve the problem either. You say yourself that you read the whole of  but you did not notice that OPN5 was mentioned quite a few times but as neuropsin. If humans find this hard it will be much harder for a script. David D. (Talk) 07:04, 14 December 2007 (UTC)
replies: text: If humans find it hard, won't it be impossible with 10,000 stubs?  How many minutes did it take you to find the secondary source, and then add a few minutes to put it in the article.  Now multiply that number by 10,000, and we're talking, what, a Man-year? AnteaterZot (talk) 07:14, 14 December 2007 (UTC)
replies: text: No, not impossible, as you know there are sources that the scripts can mine, and they are not irrelevant, just not necessarily the best (the ones for OPN5, for example were OK). How many scientists are there in this world? Even if a fraction join in that is not too much effort. That is the whole point of a massively collaborative project. if this is successful then most of the genes will be upgraded to something very useful.  At worst know one touches them and they remain a valuable source for information when linked to from other wikipedia articles. David D. (Talk) 07:36, 14 December 2007 (UTC)
replies: text: A man-year if there are no hitches, and few AfD debates. The database it's mining is from the government.  And the OPN5 citations were not OK, the bot found two that don't mention the gene at all, and one that mentioned the gene in the Literature Cited section--a citation which it failed to pick up. AnteaterZot (talk) 08:28, 14 December 2007 (UTC)

text: The first ref is a review too. I'll be the first to cheer if the bot can do better. David D. (Talk) 09:27, 14 December 2007 (UTC)
replies: text: You're right. Still, one wonders if it was a happy accident, or the design parameters of the project. I'll know more when I randomly sample some additional stubs, and now that I've had some practice at it, I should be able to do it without help. AnteaterZot (talk) 09:33, 14 December 2007 (UTC)
thread_title:  Sourcing 

message: Look at SLC9A3R2, one of the ones that was suggested to me.  If you look at the citations, many of them seem to be about the gene E3KARP instead.  I think the bot has somehow gotten out of sinc with itself, and is applying the citations to the wrong article.  Am I wrong?  If I'm right, I can't even begin to look at notability.  (In any case, SLC9A3R2 doesn't show up much in the citations.  I admit I haven't gone through it with a fine-toothed comb, since it would be a waste of time if the bot was applying the wrong citations.) AnteaterZot (talk) 05:39, 14 December 2007 (UTC)
replies: text: If you look in the protein box, there is a list of alternative names, E3KARP is one of these. Tim Vickers (talk) 05:46, 14 December 2007 (UTC)
replies: text: Ah, I was looking in the text. How about OPN5? How did the bot find those citations? AnteaterZot (talk) 05:49, 14 December 2007 (UTC)
replies: text: This citation seems to be right. From what I can see, this is all about NHERF2 aka SLC9A3R2. Of course, it interacts with a lot of other proteins.Biophys (talk) 05:51, 14 December 2007 (UTC)
replies: text: I see, the protein goes by many names. How did the bot find what I think are bad citations for OPN5 (above)? AnteaterZot (talk) 05:56, 14 December 2007 (UTC)
replies: text: Perhaps let's step back and see the forest from the trees here.  As stated above, all citations are taken from Entrez Gene (click the Pubmed link).  Even if the OPN5 references above are garbage, I think we can assume that in the vast majority of cases, references are correctly linked.  And in the rare cases when things are wrong, the bot content is easily overriden by human editors.  AndrewGNF (talk) 06:24, 14 December 2007 (UTC)
replies: text: Yes, I overlooked the alternate names.  Sorry about that.  How does one overide the bot in a case like OPN5, where it seemed to have grabbed "Opsin G"?  What about my idea of the bot only taking article which feature the gene in the title or abstract?  And my idea of limiting the genes to ones that have been in the title or abstract of one (or more) review articles?  I feel that this would address the notability concern.  AnteaterZot (talk) 06:31, 14 December 2007 (UTC)
thread_title:  Bug in citations? 

message: According to Wikipedia:Verifiability, the content of WP articles should be "verifiable", which means "that any reader should be able to check that material added to Wikipedia has already been published by a reliable source". Articles  generated by the bot satisfy this core policy twice. First, the content of the articles is supported by established scientific databases, and the links to the databases have been provided. Second, the articles cite supporting publications from scientific journals. Perhaps the title "Further Reading" is misleading and should be replaced by the title "Sources", because these are sources. There is no any other problems. As soon as the core Wikipedia:Verifiability requirement has been satisfied, the exact citation style (that is "in line" or not) is only a matter of convenience for a reader, but not a requirement. All cited sources satisfy WP:Source. Note that biological databases are reliable secondary sources.Biophys 20:50, 13 November 2007 (UTC)
replies: text: I agree with Biophys' comments regarding satisfying Wikipedia:Verifiability.  Although if we wanted to create an inline citation, we could certainly do something like this.  But I think the original version is much more concise and clear.  AndrewGNF 21:59, 13 November 2007 (UTC)
replies: text: Good answer! This is actually correct inline citation. It does not make the article any worse, but it also does not make anything better. So, that is something to avoid unless others make a big issue of it.Biophys 22:17, 13 November 2007 (UTC)

text: Thanks for your input.  First, one should note that in cases where the patterns are obviously wrong, feel free to delete the images from the infobox and set the "update_protein_box" to no.  Second, we feel that those images are of pretty high-quality (though as mentioned before I'm biased).  Moreover, I think the expression pattern in human anatomy of a given gene is an important aspect of gene function (just as important as knowing it's a kinase, for example).  So, having said all that, do you have a recommendation regarding changes to the default behavior of PBB?  AndrewGNF (talk) 16:21, 16 December 2007 (UTC)
replies: text: One problem eith the gcRMA data (RNA profile) is that it includes various tissue cultured cells and tumors. If the gene is overexpressed in one or more of those, the median is skewed. I would look for a database that only used normal human tissues. AlbertHall (talk) 18:27, 16 December 2007 (UTC)
replies: text: True, though I don't think there are so many of those samples that will substantially change the median.  (The median, of course, is rather robust to a small number of outliers.)  Having said that, we're still open to any specific suggestions/alternatives.  AndrewGNF (talk) 18:34, 16 December 2007 (UTC)
thread_title:  Verifiability issues 

message: Following up on Andrew's comment above, I added the config instructions for MiszaBot to this page. There is a 10-day timeout (adjustable). Within 24 hours it should start taking away old threads, and adding them to User_talk:ProteinBoxBot/Archives/Archive1, which I believe it is smart enough to create. See the instructions at User:MiszaBot/Archive HowTo. EdJohnston (talk) 20:58, 21 December 2007 (UTC)
replies: text: Super, much appreciated...  AndrewGNF (talk) 21:08, 21 December 2007 (UTC)
thread_title:  MiszaBot archiving 

message: As proposed by AnteaterZot above, halt the currently ongoing Version 1 and modify the bot to make a three-tiered refs list: "Review articles" (all review articles), "Futher reading" (all other Entrez links), and "External links".  
====Support====
# AnteaterZot Might I just add that having the review articles highlighted is useful beyond assessing notability, and that appearances in databases (as named below) is rather like almanac information, and does nothing to establish notability? For example, a database exists for nearly all movie actors–IMDB–but not all actors are notable. Ooh-ooh! I've got another example; a bot makes a stub for every star in the galaxy that has been given a name, has a known position, spectrum, size, whatever. Once you get beyond the brightest ones, are they notable? AnteaterZot (talk) 00:20, 18 December 2007 (UTC)
replies: text: Comment. I agree that "orphan" proteins without an established biological function are insufficiently notable for WP. But we can not easily sort them out using any simple and formal criteria. I think the best approach would be to create such articles (including olfactory receptors), look at them, and label some of them with "notability" template, just as any ordinary article. But so far, I have seen only one such potentially non-notable non-GPCR article. If a lot of such articles will begin to appear, it would mean that run "1" of the bot is close to the end. But we are still very far from that point.Biophys (talk) 20:46, 23 December 2007 (UTC)

text: I think a fair number of people have this page on their watchlist, so I wouldn't be surprised if we get a fair turnout.  OTOH, if you'd like to link here from the other relevant discussions, feel free...  AndrewGNF (talk) 23:14, 17 December 2007 (UTC)
replies: text: I can't change an archive, so I was thinking of just alerting some folks on their talk pages. Is that cool? AnteaterZot (talk) 23:41, 17 December 2007 (UTC)
replies: text: Don't see why not.  Though I pity anyone who is going to try to get up to speed "cold" by reading the discussions above and at WP:NOR and WP:N.  ;) AndrewGNF (talk) 23:49, 17 December 2007 (UTC)
replies: text: I also do not object. But if that was an AfD discusssion of a "hot" political topic, that would be considered a "forum shopping" and against WP policies.Biophys (talk) 00:15, 18 December 2007 (UTC)
replies: text: Yes, that's why I asked first, although I think it is called canvassing, not forum shopping. AnteaterZot (talk) 00:26, 18 December 2007 (UTC)
replies: text: I'm not going to ask them. If you guys want to be certain that you have consensus, consider writing them yourselves. AnteaterZot (talk) 01:09, 18 December 2007 (UTC)

text:  I'll put it on the list of things to do. If A few more people chime in that this is a great change they would like to see, then I might move up its priority on that list.. :)  JonSDSUGrad (talk) 23:42, 20 December 2007 (UTC)
thread_title:  Proposal to tag review articles 

message: # AnteaterZot Might I just add that having the review articles highlighted is useful beyond assessing notability, and that appearances in databases (as named below) is rather like almanac information, and does nothing to establish notability? For example, a database exists for nearly all movie actors–IMDB–but not all actors are notable. Ooh-ooh! I've got another example; a bot makes a stub for every star in the galaxy that has been given a name, has a known position, spectrum, size, whatever. Once you get beyond the brightest ones, are they notable? AnteaterZot (talk) 00:20, 18 December 2007 (UTC)
replies: text: Comment. I agree that "orphan" proteins without an established biological function are insufficiently notable for WP. But we can not easily sort them out using any simple and formal criteria. I think the best approach would be to create such articles (including olfactory receptors), look at them, and label some of them with "notability" template, just as any ordinary article. But so far, I have seen only one such potentially non-notable non-GPCR article. If a lot of such articles will begin to appear, it would mean that run "1" of the bot is close to the end. But we are still very far from that point.Biophys (talk) 20:46, 23 December 2007 (UTC)
thread_title: Support

message: # AndrewGNF (talk) 22:56, 17 December 2007 (UTC)
thread_title: Oppose

message: Is it a good idea to run this by people who have previously expressed their support for the bot and those who have previously expressed a concern about notability? AnteaterZot (talk) 23:06, 17 December 2007 (UTC)
replies: text: I think a fair number of people have this page on their watchlist, so I wouldn't be surprised if we get a fair turnout.  OTOH, if you'd like to link here from the other relevant discussions, feel free...  AndrewGNF (talk) 23:14, 17 December 2007 (UTC)
replies: text: I can't change an archive, so I was thinking of just alerting some folks on their talk pages. Is that cool? AnteaterZot (talk) 23:41, 17 December 2007 (UTC)
replies: text: Don't see why not.  Though I pity anyone who is going to try to get up to speed "cold" by reading the discussions above and at WP:NOR and WP:N.  ;) AndrewGNF (talk) 23:49, 17 December 2007 (UTC)
replies: text: I also do not object. But if that was an AfD discusssion of a "hot" political topic, that would be considered a "forum shopping" and against WP policies.Biophys (talk) 00:15, 18 December 2007 (UTC)
replies: text: Yes, that's why I asked first, although I think it is called canvassing, not forum shopping. AnteaterZot (talk) 00:26, 18 December 2007 (UTC)
replies: text: I'm not going to ask them. If you guys want to be certain that you have consensus, consider writing them yourselves. AnteaterZot (talk) 01:09, 18 December 2007 (UTC)
thread_title: Interested parties

message: Just to throw this out here (and I am talking for Version 2 of the bot) as an alternative to adding a whole new section to each gene page, why not just add a small bold REVIEW to each article that deserves such a tag.  It would be easy for anyone to scan the references for review articles then and make a distinction between review and non-review.  Plus it wouldn't add another section to the page (PBB has no control over page sections except on initial creation), but would still accomplish what was suggested and allow PBBv2 to make the change to all gene pages in the future that allow for changes in the citations.  It would be a non-issue to make a small change to the citation template to incorporate a "Review?" field and then PBB's code could modified to take advantage of the new option... just my .$02 JonSDSUGrad (talk) 19:47, 18 December 2007 (UTC)
replies: text:  I'll put it on the list of things to do. If A few more people chime in that this is a great change they would like to see, then I might move up its priority on that list.. :)  JonSDSUGrad (talk) 23:42, 20 December 2007 (UTC)
thread_title: Alternative Idea

message: On a completely different subject, while chasing the bot around last night, I discovered Lactoylglutathione lyase is another name for GLO1 (Glyoxalase I is a redirect to Lactoylglutathione lyase). I'm not sure, but I think that the L.L. page is about Glyoxalase I in all species, right? Nevertheless, should the bot include a link to the an EC number where a listing exists? (For an example, see ) for Glyoxalase I.) AnteaterZot (talk) 23:49, 18 December 2007 (UTC)
replies: text: It's already in the protein box, the third "identifier" at the top. It currently links to this page. David D. (Talk) 06:33, 19 December 2007 (UTC)
replies: text: I can't speak to the specific example you gave above, but more generally, better treatment of EC numbers is one of our Version 2 improvements.  While there is a slot for it in the protein box template, EC numbers currently aren't retrieved by PBB (flaw in the underlying database actually, not PBB's fault).  Especially with the parallel effort to get pages for all EC numbers, this is high on the list of improvements.  In the mean time, for pages being merged with PBB content, we make a special note to transfer EC designations when available in the old infobox to the new PBB infobox. AndrewGNF (talk) 16:59, 19 December 2007 (UTC)
replies: text: Great. I strongly recommend to change the colors of some of the infoboxes so that human gene pages can be rapidly distinguished from these other page types. Beige is so boring. AnteaterZot (talk) 00:31, 20 December 2007 (UTC)
replies: text: Have at it...  Changes to how the underlying templates are rendered can be done by anyone, and PBB doesn't care one bit.  So if anyone with an eye for that sort of thing wants to mess around with that, you'll get no objection from me.  (Well, not before I see the change anyway...) AndrewGNF (talk) 00:56, 20 December 2007 (UTC)
replies: text: Color is changed. AnteaterZot (talk) 02:09, 20 December 2007 (UTC)
replies: text: I can't say that I love the new colors, but I don't hate them either.  I'm willing to let it stew for a while to see if it grows on me.  Other than that, let's see how the court of public opinion reacts.  (Maybe we can do seasonal colors -- red and green in December, yellow and purple around easter, orange and black around halloween...)  ;) AndrewGNF (talk) 02:21, 20 December 2007 (UTC)
replies: text: I tried out a few colors. I could try a few more. It's tricky; you have to avoid grey, beige, dark colors and blues. I avoided bright colors too. I wanted something that would be unobtrusive but would look different from the protein template. AnteaterZot (talk) 02:30, 20 December 2007 (UTC)
replies: text: I would write more, but my wife would tell me I have no basis on which to comment on the aesthetics of color.  AndrewGNF (talk) 02:44, 20 December 2007 (UTC)

text: Gotta say, I'm not much one for the "dusty rose" color - the contrast just isn't there.. I kinda liked the original gold.. The best thing would be to adjust the background grey and the rose color at the same time and see if you can get a nice combo that way.  I don't have time to tinker with the colors right now or I would give it a shot.. :) JonSDSUGrad (talk) 23:55, 20 December 2007 (UTC)
replies: text: Agree with JonSDSUGrad. I also like old color better.Biophys (talk) 00:38, 21 December 2007 (UTC)
replies: text: Given lukewarm reception, I reverted the color change.  But still open to alterations.  Take further discussion over at Template_talk:GNF_Protein_box?  AndrewGNF (talk) 00:51, 21 December 2007 (UTC)
replies: text: My goal was to make the color different from the protein family infoboxes. I was not wedded to the dusky rose. I'll try out a few other colors, nothing permanent need be assumed. AnteaterZot (talk) 01:09, 21 December 2007 (UTC)
replies: text: Since this isn't really a PBB issue (and since this talk page is long enough), let's take any followups to Template_talk:GNF_Protein_box#Color_scheme.  Incidentally, if anyone readily knows how to configure one of the archiving bots to scan this page and wants to do us all the great favor of setting it up, that would be great... AndrewGNF (talk) 01:32, 21 December 2007 (UTC)

text: My word, glyoxalases! How exciting. To be completely clear EC 4.4.1.5 applies to all glyoxalse I enzymes except those in the Trypanosomatids, since these organisms contain a novel trypanothione-dependent glyoxalse system. This was discussed first in the particularly fine article  from a small lab in Dundee. Tim Vickers (talk) 16:44, 21 December 2007 (UTC)
replies: text: So do you support Dundee or Dundee United? Or are you an atheist :) David D. (Talk) 18:08, 21 December 2007 (UTC)

text: I'm agnostic, I'm not sure if either team is really better than the other. :) Tim Vickers (talk) 12:46, 23 December 2007 (UTC)
thread_title:  [[EC number]] 

message: If you look at Special:Whatlinkshere/Template:Protein you'll see many articles that already exist for genes the bot might create/has created a stub for. AnteaterZot (talk) 02:09, 20 December 2007 (UTC)
replies: text: Yes, we should look at these pages and mark some of them for merging. But this will be most efficient after completion of the first run by the bot. I think  ProteinBoxBot is running very smoothly. Almost half of links to human genes in protein family pages now appear in blue. Good job! Let's keep the bot running.Biophys (talk) 20:32, 21 December 2007 (UTC)
replies: text: I went through a few logs just in case. Not only it is much faster now, but it allows a much better quality work, when an editor can focus on real alternative names of each proteins indicated in the UniProt entry, instead of dealing with "junk" gene names in Entrez gene. Unfortunately, UniProt links are sometimes missed by the bot. Note that UniProt codes are included in each Entrez Gene entry, so I do not know what is happening. Otherwise, everything if fine. That is a significant improvement over the previous version.Biophys (talk) 01:50, 23 December 2007 (UTC)
replies: text: Glad you like it, and thanks again for the help.  Just to note, half of the improvement is that we're skipping most of the "hard cases" that will need more manual attention later.  But you're right, doing the low-lying fruit first really speeds things up and makes volunteering much easier.  (Sorry, couldn't resist the plug.)  We'll check on the Uniprot issue.  AndrewGNF (talk) 01:57, 23 December 2007 (UTC)
replies: text: Where is the list of difficult/missed cases? Is not it in a log?Biophys (talk) 01:59, 23 December 2007 (UTC)
replies: text: We've actually just set them aside for the time being.  Anything that has a high likelihood of hitting an existing page, we'll save for later.  The ones that we think do not have an existing page are easy, so we'll get through those all first.  (Of course, we falsely allow some pages to pass, which is why we still need volunteers to double check the work.)  Anyway, it's easier if all the easy cases are lumped together and all the hard cases are lumped together.  And obviously, might as well do the easy cases first... AndrewGNF (talk) 02:12, 23 December 2007 (UTC)
replies: text: I agree. It just would be good to make a log file with problematic cases somewhere. But let's keep bot running in present state.Biophys (talk) 02:46, 23 December 2007 (UTC)

text: My count is 4552, after limiting to the main namespace.  This link is the one I use...  The order listed by "What links here" is not the order created, but it seems to be a rough ordering of "importance" (# links? # edits?).  Anyway, WP's order of importance roughly agrees with PBB's order of creation, but not exactly... FWIW... AndrewGNF (talk) 05:41, 24 December 2007 (UTC)
replies: text: Just do not rely too much on this formal ranking. At least two thirds of important/notable human proteins/genes are missing now.Biophys (talk) 17:01, 24 December 2007 (UTC)
thread_title:  List of existing proteins 

message: I made a stub for Metastasis suppressor, then linked it to a number of pages the bot made. I then turned off the summary update to prevent the bot from overwriting my changes. Was that necessary? Or should I not have done that? AnteaterZot (talk) 05:54, 23 December 2007 (UTC)
replies: text: If you don't modify the text enclosed in the PBB summary template, as you have done on TIMP1, you can safely keep its update status on "yes". The bot updates only specific sections marked off by templates. By the way, I'm glad to see new articles filling the gaps between gene pages ;) --Banus (talk) 10:09, 23 December 2007 (UTC)
thread_title:  Turning off summary update 

message: Would it be possible for this bot to upload to the Commons instead of to here? —Remember the dot (talk) 19:51, 5 January 2008 (UTC)
replies: text: Yes, that is a change we are considering for version 2.  A quick scan of WP:MITC suggests there are many issues to consider if we are to do it right.  The plan for the immediate future is to finish the previously-approved version 1 run.  AndrewGNF (talk) 17:09, 7 January 2008 (UTC)
thread_title:  Commons 

message: You new page creations are not flagged as bot creations, making it impossible to hide them on new page patrol. This is a bit annoying. Could this be solved? Fram (talk) 15:55, 14 January 2008 (UTC)
replies: text: Thanks for the note.  Yes, we'll definitely look into this.  AndrewGNF (talk) 19:23, 14 January 2008 (UTC)
thread_title:  Bot flag 

message: In case anyone is interested, the PBB effort has been blogged...   AndrewGNF (talk) 19:24, 14 January 2008 (UTC)
replies: text: Great, an very interesting discussion. Tim Vickers (talk) 19:37, 14 January 2008 (UTC)
replies: text: Was a more solid article about PBB submitted anywhere? I did not know about Proteins Wiki. Please see organization of their protein articles: . It includes "Protein interactions", "Domain structure" and other sub-headings missing in PBB articles.Biophys (talk) 21:16, 14 January 2008 (UTC)
replies: text: Gene/protein wiki efforts shouldn't be judged based on the stubs, whose primary purpose is to seed contributions from the larger (human) community.    AndrewGNF (talk) 18:32, 15 January 2008 (UTC)
replies: text: Right, I agree 100%. Also, there is no questions that your stubs are much better than their stubs. I just wanted to tell that everyone (including authors of Protein Wiki) understands the  importance of domain structure and other information that could be automatically extracted from the databases by your bot, but was not  extracted. That could be criticized by reviewrs if you submit a paper. But you know better. Perhaps it has been already published. So I asked.Biophys (talk) 19:01, 15 January 2008 (UTC)
replies: text: Yup, no harm in the reminder and you also know it's on our V2 to-do list.  But the real point actually is not that our stubs are better.   (In fact, perhaps the Proteins Wiki ones are better for some people for the differences you noted.)  The point I think is that the community here is better/bigger.  Where to put the stub is more important than what's in it...  (no news on the manuscript yet...)  AndrewGNF (talk) 19:10, 15 January 2008 (UTC)
thread_title:  Blogosphere 

message: I've noticed that articles generated by ProteinBoxBot tend to have large blank spaces in between the infobox and the initial text. Is there anyway that your bot can be reconfigured so that it doesn't create these blank spaces?--69.118.143.107 (talk) 23:34, 21 January 2008 (UTC)
replies: text: Thanks for the note.  We're in the processing of finishing up round 1 of the bot run, but I've added your note to the Version 2 specs.  Cheers, AndrewGNF (talk) 01:37, 22 January 2008 (UTC)
thread_title:  blank spaces 

message: An image or media file that you uploaded or altered, :Image:PBB GE NIPA1 gnf1h07157 at fs.png, has been listed at Wikipedia:Images and media for deletion. Please see the discussion to see why this is (you may have to search for the title of the image to find its entry), if you are interested in it not being deleted.  — Cuyler91093 - Соитяівцтіоиѕ 05:51, 27 January 2008 (UTC)
thread_title:  Image:PBB GE NIPA1 gnf1h07157 at fs.png listed for deletion 

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 any questions, please feel free to ask them at the media copyright questions page. Thanks again for your cooperation. Flominator (talk)  —Preceding comment was added at 08:08, 25 January 2008 (UTC)
replies: text: Thanks for the note.  As you noted, we reference  for copyright info, and the first line says "The contents of PDB are in the public domain."  This was the basis of tagging all images from the PDB with .  Is that not sufficient?  I also have a vague recollection that Tim had some direct contact with PDB folks, so perhaps he will chime in too.  AndrewGNF (talk) 12:47, 25 January 2008 (UTC)

text: Thanks for the response Tim.  In my early morning stupor, I didn't notice the link to the media copyright questions page.  I'll take the rest of the discussion over there.  AndrewGNF (talk) 18:20, 25 January 2008 (UTC)
thread_title:  Image copyright problem with Image:PBB Protein NFAT5 image.jpg 

message: Another editor has added the "" template to the article IQSEC1, suggesting that it be deleted according to the proposed deletion process. All contributions are appreciated, but the editor doesn't believe it satisfies Wikipedia's criteria for inclusion, and has explained why in the article (see also Wikipedia:What Wikipedia is not and Wikipedia:Notability). Please either work to improve the article if the topic is worthy of inclusion in Wikipedia or discuss the relevant issues at its talk page. If you remove the  template, the article will not be deleted, but note that it may still be sent to Wikipedia:Articles for deletion, where it may be deleted if consensus to delete is reached.  BJBot (talk) 20:59, 26 January 2008 (UTC)
replies: text: I added some more context, incorporated some of the refs from "Further reading" into the article, and removed the template. Tim Vickers (talk) 01:05, 27 January 2008 (UTC)
replies: text: The problem here is that Tim can't do that for every article.  If these articles are allowed to live then experts will be attracted to make significant contributions to wikipedia. If everyone os going to prod these articles it will be a nightmare to keep repeating the same rationales. We need to figure out a way to stop these prods without having to manually update these articles so they will survive long enough to attract new editors. David D. (Talk) 01:46, 27 January 2008 (UTC)

text: One proposed deletion out of several thousand articles over six months, that's not something I'm worried about. Tim Vickers (talk) 01:48, 27 January 2008 (UTC)
replies: text: Wow, there are several thouand already! I have not been keeping my eyes open. David D. (Talk) 07:25, 27 January 2008 (UTC)
replies: text: As of right now, there are 8341 pages that use .  A semi-current list can also be found here.  AndrewGNF (talk) 20:56, 27 January 2008 (UTC)
thread_title:  [[:IQSEC1]]