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Gene Wiki – Discussion |
Discussion moved from Talk:Mammalian target of rapamycin (see also Talk:BRCA1#Interactions):
The Interactions section has a huge number of references. Can we split the list (and references) into a separate mTOR interactions article or similar ? Rod57 ( talk) 18:26, 6 December 2010 (UTC)
{{
cite web}}
: Cite has empty unknown parameter: |coauthors=
(
help)I think the actual problem is the poor presentation of interactions as tediously long lists, and propose converting them to prose. See discussion at: talk:Converting interactions-sections to prose. Mikael Häggström ( talk) 07:00, 15 May 2011 (UTC)
An Error has occurred retrieving Wikidata item for infobox
This template causes this to appear:
But obviously it should instead have said this:
with an en-dash rather than a hyphen (see WP:MOS). As far as I can tell I can't edit this thing. Could whoever tends to this thing fix the punctuation error? Michael Hardy ( talk) 23:15, 12 February 2011 (UTC)
Could somebody sort out Complementarity determining region? Part of it was deleted some time ago (including refs), then it was expanded a bit, and I just can't sort out what is constructive and what not. Thanks, ἀνυπόδητος ( talk) 10:59, 13 February 2011 (UTC)
What is the best way to handle when one is referring to several isoforms of a gene. This came up in the FIG4 page where a link to yeast Atg18 was pointed to one of four mammalian WIPI proteins. For protein families, should a new page be generated? Davebridges ( talk) 22:57, 8 March 2011 (UTC)
PREP (gene) is a article completely bot-edited, it seems equivalent, but different from, Prolyl endopeptidase. Can some-one have a look at those two articles? -- Havang(nl) ( talk) 10:36, 12 March 2011 (UTC)
What is "A Proliferation Inducing Ligand (APRIL)" mentioned in B-cell activating factor and Belimumab, among other pages? HGNC knows two proteins with the synonym APRIL: ANP32B and TNFSF13. I suspect the latter, but could someone (i. e. most likely Boghog) confirm this? Thanks, ἀνυπόδητος ( talk) 19:53, 13 March 2011 (UTC)
A file that you uploaded or altered, File:PBB Protein MRPL11 image.jpg, has been listed at Wikipedia:Files 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. Thank you. Skier Dude ( talk) 03:04, 28 April 2011 (UTC)
A draft MCB Style Guide for gene/protein articles has been written. Since this style guide in principle applies to all Gene Wiki articles, I thought I should mention it here. Contributions and comments are welcome. Boghog ( talk) 20:23, 19 May 2011 (UTC)
There's a small escaping bug in the GeneWikiGenerator: "<" is shown as "& l t ;" (sans spaces), e.g. currently http://biogps.gnf.org/GeneWikiGenerator/#goto=genereport&id=29911 . MichaK ( talk) 15:54, 31 May 2011 (UTC)
Sorry to dig up an old issue, but I recently went through a bunch of gene/protein articles and changed the wording of all the lead sentences ( for example), not knowing that there was an agreed style for that first sentence. I think the problem was that it's not clear from the lead:
that the article is meant to address both the gene and the protein.
I think it would be a good idea to tweak this slightly to prevent another editor from coming through and making the same mistake. I was thinking maybe a hidden notice at the top of the page, like <!-- The lead sentence should be in the format:<recommended UniProt name> is a protein that in humans is encoded by the <approved HUGO gene symbol> gene.--> or adding a sentence at the top similar to a disambiguation notice, along the lines of "This article addresses both <protein> and <gene>. I don't know, though. Thoughts? Kerowyn Leave a note 06:33, 24 June 2011 (UTC)
Main subunit of cytochrome c oxidase states that COX1 and MT-CO1 contain this peptide. Does COX1 refer to PTGS1 here? Furthermore, COI (which is also a synonym of MT-CO1) links to a disambig and CO1 (??) to carbon monoxide which is rather unlikely to contain a polypeptide. Could someone clarify? Thanks -- ἀνυπόδητος ( talk) 06:45, 20 July 2011 (UTC)
(cross-post from the semi-active WP:WikiProject Cell Signaling) Any objections if I propose deletion of the signal transduction stub type? Category:Signal transduction stubs contains a rather arbitrary collection of 13 pages, most of which could go into Category:Receptor stubs or Category:Transmembrane receptor stubs. Thanks, ἀνυπόδητος ( talk) 17:15, 12 September 2011 (UTC)
It's come to my attention that ProteinBoxBot, which maintains this project's infoboxes, uses a curious template known as {{
PBB}} to add them to articles. For some reason this template insists on adding a wrapping table around the infobox and sticking an [edit] link above it, which not only pushes the infobox down articles but is also completely unnecessary as the infobox code supports an edit link anyway. ProteinBoxBot should instead be adding the name =
attribute to the infobox pages themselves. Adding | name = PBB/9353
to {{
PBB/9353}}, for instance, results in the output shown at {{
PBB/testcases}} (an unobtrusive link at the bottom of the template).
user talk:ProteinBoxBot redirects here, so if the ProteinBoxBot maintainers need any further details then please point them at my talk page. This is a trivial change which should positively impact the appearance and accessibility of thousands of articles.
Chris Cunningham (user:thumperward) - talk 19:58, 14 September 2011 (UTC)
{{{name}}}
parameter, I think you misunderstand its purpose: it is not the same as {{{Name}}}
(note the change in capitalisation) which gives the subject title, but in fact needs to refer to the current page title in order for the navbox magic to link to the correct view / talk / edit pages. Anyway, the first thing to do is to get ProteinBoxBot to add the links in question: once that's done, I'll update {{
PBB}} to take them into account. I've pinged the bot's owners with a link to this discussion.
Chris Cunningham (user:thumperward) -
talk 09:27, 15 September 2011 (UTC)PBB/9353
field, I'm a little hesitant to have both 'Name' and 'name' fields that do very different things. What if we put it under 'path' or 'PageLocation', or something similar? Boghog, I'm still not 100% sure I understand your suggestion regarding PAGENAME -- can you clarify? Cheers,
AndrewGNF (
talk) 16:38, 15 September 2011 (UTC) AndrewGNF: I agree that having both {{{name}}}
and {{{Name}}}
is confusing. If you want to go with {{{path}}}
for the parameter then I'll update {{
GNF_Protein_box}} to use that for the navbar links instead.
Chris Cunningham (user:thumperward) -
talk 06:10, 16 September 2011 (UTC)
{{{path}}}
parameter on its next run, which should be sometime in the next few days. I'll let
Chris know so he can change {{
GNF_Protein_box}} at that time.
Pleiotrope (
talk) 18:08, 16 September 2011 (UTC){{{path}}}
parameters and these are working fine, so I've updated {{
PBB}}. See the new, cleaner look on one of the new pages such as
TTLL3. Thanks, folks.
Chris Cunningham (user:thumperward) -
talk 11:41, 23 September 2011 (UTC)Albondin (gp60) is a sub-stub that might profit from a gene infobox. Or there already might be a gene article to which it could be merged. Thanks, as ever, ἀνυπόδητος ( talk) 08:08, 15 September 2011 (UTC)
Hello, I dropped a message with question here : http://en.wikipedia.org/wiki/Template_talk:GNF_Protein_box#IDs. Thanks :) Anthere ( talk) 07:12, 20 September 2011 (UTC)
The GeneWikiGenerator is down (504 Gateway Time-out). There has been a recent flurry of interest. Also is there any chance that the bugs first described here could be fixed? Thanks. Boghog ( talk) 17:15, 23 September 2011 (UTC)
We're soliciting feedback for the use of a new template that should be pretty useful on GeneWiki pages over at the village pump and we'd like your opinions. The example we use there is targeted to a broader audience, but we have some GeneWiki specific examples and motivation here: WP:Gene Wiki/SWL proposal. Thanks, Pleiotrope ( talk) 17:15, 19 October 2011 (UTC)
Since wikipedia is supposed to be useful to non-specialists, I went and added a whole bunch of wikilinks to DLX1: humans homeobox transcription factor Drosophila TGF-β craniofacial differentiation neurons forebrain chromosome 2 Alternatively spliced isoforms. Then I noticed that PBB updates the text and my wikilinks could get deleted pretty soon.
Is is worth adding some wikilinking ability to PBB so it can do this automatically to (the first appearance of) biology buzzwords? (Then you could get rid of the "require_manual_inspection" flag I added.)
I'm not quite sure what The Right Thing is here. Could PBB at least be changed to preserve the wikilink if the linked word is still in the replacement text? 71.41.210.146 ( talk) 16:56, 7 November 2011 (UTC)
A tag has been placed on Template:PBB/HP1BP3, requesting that it be speedily deleted from Wikipedia. This has been done for the following reason:
Under the criteria for speedy deletion, articles that do not meet basic Wikipedia criteria may be deleted at any time.
If you think that this notice was placed here in error, contest the deletion by clicking on the button labelled "Click here to contest this speedy deletion". Doing so will take you to the talk page where you will find a pre-formatted place for you to explain why you believe the page should not be deleted. You can also visit the page's talk page directly to give your reasons, but be aware that once tagged for speedy deletion, if the page meets the criterion, it may be deleted without delay. Please do not remove the speedy deletion tag yourself, but don't hesitate to add information to the page that would render it more in conformance with Wikipedia's policies and guidelines. If the page is deleted, you can contact one of these administrators to request that the administrator userfy the page or email a copy to you. Bulwersator ( talk) 08:40, 19 December 2011 (UTC)
Linked from / mentioned in a number of articles [1] [2]. NG2 is about a Puerto Rican Salsa duo which is probably unrelated. Anyone willing to write a bit about these? -- ἀνυπόδητος ( talk) 14:01, 20 December 2011 (UTC)
A file that you uploaded or altered, File:PBB Protein GSTA2 image.jpg, has been listed at Wikipedia:Possibly unfree files because its copyright status is unclear or disputed. If the file's copyright status cannot be verified, it may be deleted. You may find more information on the file description page. You are welcome to add comments to its entry at the discussion if you are interested in it not being deleted. Thank you. Stefan2 ( talk) 23:58, 16 January 2012 (UTC)
A file that you uploaded or altered, File:PBB Protein GSTA1 image.jpg, has been listed at Wikipedia:Possibly unfree files because its copyright status is unclear or disputed. If the file's copyright status cannot be verified, it may be deleted. You may find more information on the file description page. You are welcome to add comments to its entry at the discussion if you are interested in it not being deleted. Thank you. Stefan2 ( talk) 23:58, 16 January 2012 (UTC)
Further to the suggestion by BogHog that a discussion on my talk page (see here) would benefit from wider input, I'm bringing it here. In summary, I have started on a project to populate as many of the Gene Wiki pages as possible with "functional" information gleaned from model organisms. I guess the wider goal is to bring phenotypes to the Gene Wiki in as standardized a manner as possible. I think this is important, because much of the content we have on these genes are from various model organisms, and currently the information on the pages are a bit of a mishmash of references to mouse and human, and occasionally fly and yeast, orthologues. Orthologous genes do not necessarily share all the same characteristics between species, so there is a potential to mislead readers unless we are careful with these distinctions, and generally we haven't been.
So I have been creating "model organism" sections where that information, when present, can be sectioned off from the information on human genes. I have also been including new content pulled from the set of standarized mouse KO lines, generated by the International Knockout Mouse Consortium, and where available the standardized phenotypic analysis carried out on these animals by the various international phenotyping centres (accompanied by a collapsed summary table). A nice example of this is SLX4, though there are many more genes with much less interesting phenotypes (e.g. Ciliary neurotrophic factor receptor). There are currently around 500 genes with this information available in the mouse, and I plan to add them all to their Gene Wiki pages, and many more should be generated over the next few years. I should point out that I work at one of the phenotyping centres (The Wellcome Trust Sanger Institute). Though I am not directly involved the phenotyping project, I have been able to get the support of their informatics team. So I am starting with their data because I can generate it easily in a wiki-accessible format. It is my intention, however, to move on to the lines from the other centres (and try and convince them to provide me Wiki-friendly data dumps).
The bigger picture, of course, is to try and encourage the contribution of other model organism information for each gene, thereby increasing the knowledge base on Wikipedia. I'm content to continue adding these by hand over the coming months (and probably years) as I think there is value in a human parsing the information to identify the model organisms derived content, and then writing the section in a way that suits the article. However, there is also scope - as BogHog suggests - for bot assistance or merging some content to the infobox. I'm happy to defer to the consensus on that and any suggestions on how to proceed. But if there are no major objections to this, in the meantime I will continue to work on these one at a time. Rockpocke t 00:33, 27 January 2012 (UTC)
The message here pointed out some issues with the description of images uploaded by PDBbot, for example the previous description for Protein_CREBBP_PDB_1f81.png: "Structure of the CREBBP protein. Based on PyMOL rendering of PDB 1f81." The main issue is that PDB 1f81 corresponds to a fragment of the CREBBP protein, and a statement like "Structure of the CREBBP protein" could plausibly be interpreted to say that the image shows the entire protein. Also, there is nothing to indicate that 1f81 is from a mouse protein, and is not from a human -- here again, the omission of a detail could lead the reader to assume the image shows something it does not.
These issues potentially exist with many of the ~2,500 images uploaded by PDBbot. I updated the description of the image in question here; it now reads: "Structure of the TAZ2 domain (amino acids 1764-1850) of the CREBBP protein, as expressed in the common house mouse (Mus musculus). Based on PyMOL rendering of PDB 1f81". The information needed for that expanded description exists as structured data in the PDB entry for 1f81. I think most of the information needed for similarly expanded descriptions for all PDBbot images also exists in corresponding PDB files -- i.e., the range of residues depicted in the structure, the common and scientific name of the source organism.
Are there any issues with the revised description above? Does a description close to that form seem applicable to all PDB files? Thanks in advance for any feedback. Emw ( talk) 04:06, 13 March 2012 (UTC)
Hi! Concering the lead sentence in Gene Wiki articles, as discussed here and here, we have tried to make clear that these articles are not only about the human gene/protein, but also orthologs that exist in other species. The wording that was reached through consensus is perhaps a little awkward, but it is both accurate and concise:
I recently stumbled upon GLmol, which enables in-browser 3D manipulation of chemical structures as shown here, and was thinking to myself how neat it would be if something like that could be integrated into Wikipedia's protein infoboxes. GLmol use WebGL, a new web technology that puts OpenGL (the 3D engine used by PyMOL) into modern browsers. Ideas for using Jmol to do this have been brewing for a while (see here and here), but WebGL might be a worthwhile alternative to consider.
I see a few obstacles for implementing interactive WebGL-enabled PDB structures in Wikipedia infoboxes, along with possible solutions:
Does this seem like something worth pursuing? What are others' thoughts? Emw ( talk) 04:06, 13 March 2012 (UTC)
A prototype of this feature is available at http://pdbhandler.wmflabs.org. I've developed the feature as a MediaWiki media handling extension named "PDBHandler". It enables interactive 3D models of proteins and DNA on MediaWiki deployments like Wikipedia without the need for browser plug-ins. For browsers that don't support WebGL or have it enabled, a static image of the structure is shown instead of an interactive model. Some background that informed the development of the extension is in a discussion thread on the wikitech-l mailing list here.
Any feedback would be appreciated. I'll be working on this extension all day Tuesday and/or Wednesday at the hackathon in Wikimania 2012, so any input today or tomorrow is particularly welcome.
This feature loads 3D models only after the article's text and other media is ready and displayed on the user's browser, so users don't need to wait for the 3D model to finish loading to begin reading the article. In this sense, PDBHandler does not increase articles' page load time. To minimize the time needed to load and render the 3D models themselves, I've developed a custom compression scheme for PDB files that decreases their gzipped file size by roughly 30-70%.
The static images of structures shown for users that don't have WebGL enabled in their browser are identical to the kind produced by PDBbot. The static image is generated immediately after the PDB file's upload by modified PDBbot code that runs on a MediaWiki server. This approach doesn't have the disadvantage of relying on a remote third-party web service, and got favorable feedback from MediaWiki developers on IRC and the mailing list (e.g. here) relative to the remote-server approach.
An early prototype had a favorable user experience review from Wikimedia Foundation staff. It was decided that, for the extension's initial release to Wikipedia, interactive 3D models would an opt-in feature -- i.e., they would need to be manually enabled by users in their account preferences/'My preferences' page. The default behavior for the initial release, where users had not explicitly opted in, would be to show the static image representations of structures where an article had a PDB file wikilinked, e.g. [[File:1MBO.pdb]].
The feature has some loose ends, but I hope to mostly tie those up next week. I'll update here with news on the extension. Thanks in advance for any feedback on the prototype. Emw ( talk) 18:33, 8 July 2012 (UTC)
For {{ PBB/6790}}, several GO annotations appear multiple times in the list: e.g. centrosome, spindle, mitotic cell cycle. What's going on there? As an aside, how often are the GO annotations updated? MichaK ( talk) 10:36, 22 May 2012 (UTC)
There seems to be a major bug in the {{ PBB}} template. See, for example, CD20 -- the beginning of the article now reads: , {{{1}}}, {{{1}}}, Hide Hide, </a> </a>, , Membrane-spanning 4-domains, subfamily A, member 1 Rendering based on PDB 1S8B. Available structures PDB Ortholog search: PDBe, RCSB , {{{1}}}, {{{1}}}, {{{1}}}, {{{1}}}, {{{1}}}, , {{{1}}}, {{{1}}}, {{{1}}}, {{{1}}}, {{{1}}}, MyPDB MyPDB, , {{{1}}}, {{{1}}}, Hide Hide, </a> </a>, , [show]List of PDB id codes , , , {{{1}}}, {{{1}}}, {{{1}}}, {{{1}}}, {{{1}}}, {{{1}}}, {{{1}}}, {{{1}}}, {{{1}}}, , {{{1}}}, , {{{1}}}, Username: Username: , {{{1}}}, Password: Password: ...etc., etc. Pjbradle ( talk) 16:42, 30 May 2012 (UTC)
I am in contact with the National Center for Biotechnology Information (who run web services like PubMed Central) over them providing references in a way that allows for easy copy-pasting into Wikipedia articles (similar to what Europeana does or the Biomedical citation maker). Where would be the best place to discuss what Wikipedia template formats (e.g. {{ Cite web}}, {{ Cite journal}}, {{ Citation}}, {{ Cite book}}) would be best to implement at what NCBI projects? Thanks for any pointers. Please reply at WikiProject NIH.
Another point of interest is how NCBI content could be used to update infoboxes (or even article text), similar to what PBB does - what is the best place to discuss such matters? -- Daniel Mietchen - WiR/OS ( talk) 04:00, 18 July 2012 (UTC)
Hi. I saw this Nature Communications article (as widely reported), and so searched for MIR941-1, which was created today - that article has some sort of a {{ PBB}} problem at the top, (maybe just a remnant that the bot is leaving behind?) and too much whitespace under the intro-sentence - both should probably be fixed at the source-level. This is mostly just a note for the bot maintainer ( User talk:ProteinBoxBot redirects to here), but also a pointer towards interesting articles (both ours and Nature's). HTH. — Quiddity ( talk) 18:59, 23 November 2012 (UTC)
A bot request to create systematic redirects for Gene Wiki articles so that they are easier to located has been submitted here. Comments and suggestions are welcome. Boghog ( talk) 05:02, 2 January 2013 (UTC)
it's not working for ARGLU1. the gene id is correct, so no clue as to what's happening. regards, FoCuSandLeArN ( talk) 13:51, 5 February 2013 (UTC)
Similar problem over at C9orf16 (gene). Brightgalrs (/braɪtˈɡæl.ərˌɛs/) [1] 17:28, 17 May 2013 (UTC)
Another ATXN7L2 (gene) Brightgalrs (/braɪtˈɡæl.ərˌɛs/) [1] 01:25, 8 June 2013 (UTC)
Having just discovered this portal, it seems like it belongs in the Project namespace. According to WP:Portal, "The idea of a portal is to help readers and/or editors navigate their way through Wikipedia topic areas through pages similar to the Main Page." This page seems to be more of a WikiProject. -- Ypnypn ( talk) 15:19, 26 May 2013 (UTC)
Gang -- Look at this page as an example: /info/en/?search=Ubiquitin#Human_proteins_containing_ubiquitin_domain In that section "Human proteins containing ubiquitin domain" I would like to link to wikigenes.org for the genes that do not have wikipedia pages. For example, UBL7 has no wikipedia page but does have a page here: http://www.wikigenes.org/e/gene/e/84993.html
Is the goal to link to wikigenes.org? Or some other gene wiki? How to do so in wiki code? JesseAlanGordon ( talk) 14:59, 9 July 2013 (UTC) Jesse Gordon, July 9, 2013
If you have ideas or suggestions as to which data NCBI should make available about traffic they get from Wikimedia servers, please list them here. Thanks! -- Daniel Mietchen ( talk) 21:21, 25 October 2013 (UTC)
Article AAVS1 (gene) was recently created by User:ProteinBoxBot and it includes two templates that don't exist: Template:PBB/17 and Template:Gene-17-stub. -- Derek Andrews ( talk) 01:51, 11 November 2013 (UTC)
The BioGPS for generating new Gene Wiki articles has been down some time. There are still ~10,000 gene to go. :-) Boghog ( talk) 07:45, 11 November 2013 (UTC)
Hi. ProteinBoxBot is making a large number updates that seem to be in error. See for example diff. Regards Boghog ( talk) 10:42, 15 November 2013 (UTC)
This change has been corrected. Uniprot had a misconfigured mirror which accounted for the request bodies being injected in their response. I updated our bot to fix the incorrect pages that were introduced and all seems back to normal. Cheers x0xMaximus ( talk) 21:39, 16 November 2013 (UTC)
This is mentioned in Pirinixic acid. Is this the same as PNPLA2, as the link in Serine hydrolase suggests? -- ἀνυπόδητος ( talk) 12:28, 25 November 2013 (UTC)
In the course of editing underlinked articles, I've discovered that the PBB template for HMGCS2 isn't working, and I don't know how to fix it...thought I should let you know. WQUlrich ( talk) 00:25, 26 November 2013 (UTC)
Is this also encoded by DRD2? If yes, should it be merged to Dopamine receptor D2? If no, should it have an infobox? -- ἀνυπόδητος ( talk) 08:40, 9 February 2014 (UTC)
Well, they are redirected, but it would be quicker and cause less traffic if the URL http://www.informatics.jax.org/searches/accession_report.cgi?id=MGI:{{{1}}} in {{ MGI}} were changed to http://www.informatics.jax.org/marker/MGI:{{{1}}}. I haven't found evidence that this is true for all pages, and given the high visiblity of the template, I'd rather leave the change to somebody else, i.e. Boghog. -- ἀνυπόδητος ( talk) 08:40, 9 February 2014 (UTC)
This article's trying to transclude a non-existent template (that doesn't seem to have been deleted previously, so maybe it never existed?), but it's not some sort of vandalism or accidental on-page breakage (no edits since shortly after the bot created it). Facing the Sky ( talk) 16:36, 1 March 2014 (UTC)
I can't find anything about this cytokine(?). The refs are about macrophage migration inhibitory factor and platelet activating factor as far as I can see. -- ἀνυπόδητος ( talk) 19:46, 2 December 2014 (UTC)
CACNA2D3 and CAMK1D both contain nonexistent subtemplates of Template:PBB. I can see how I would create those subpages using Template:GNF Protein box, but if ProteinBoxBot can instead that would be even better.— Neil P. Quinn ( talk) 17:33, 11 January 2015 (UTC)
For several weeks now, the BioGPS GeneWikiGenerator has not been able to create Wikipedia pages (failed creating both PBB template and GeneWiki article, Status: creation failed). One could manually create the pages by copy and pasting the output of GeneWikiGenerator into Wikipedia. Can someone take a look at this? Thanks. Boghog ( talk) 08:08, 3 April 2015 (UTC)
I am not sure where to post this request, but I saw on the Ideas Page that additional links are planned in the future for the protein box. I wanted to ask if there was a possibility to add another source to this list. Specifically I would like to suggest Genevisible which is a free resource for finding the top 5 expressing tissues/cancers/perturbations for a given gene. I will be honest here and state that I am one of the maintainers of that resource and am willing to help get a dynamic plot working (something akin to the GeneAtlas plots already in the protein box) should there be interest for it. However, I would already be grateful if a direct link from a protein/gene page to its relevant entry on our resource was added to the protein box. Here is an example for HP1BP3. I am ready to answer any questions you might have regarding this and would gladly help in implementing/testing the feature should it be accepted. Ovoggen ( talk) 11:45, 30 July 2015 (UTC)
Hi! Just wanted to note that PSMA8 is the only one of the {{ Proteasome subunits}} that hasn't got an article. -- ἀνυπόδητος ( talk) 08:50, 18 October 2015 (UTC)
Hi, what do i have to do to get parts of the reviewed items from UniprotKB (accession number, protein name, gene name, organism, GO - molecular and biological function, keywords, length, mass and sequence) into wikidata? A lady at UniprotKB told me that you already have their permission. Please see the discussion there, all the best, -- Ghilt ( talk) 21:59, 9 May 2016 (UTC)
Hi,
I would like to import drug-protein (drug-target, drug-enzyme, etc) interactions to gene_wiki from DrugBank. Would the gene_wiki community be interested in this, and, if so, what is the best way to import this data.
Thank you for your help.
Crowegian ( talk) 04:33, 24 May 2016 (UTC)
C11orf52 is an orphaned protein/gene article without an infobox. Thanks as always, Boghog! -- ἀνυπόδητος ( talk) 09:49, 10 September 2016 (UTC)
We are delighted that we have been awarded a WMF grant for WikiFactMine - a project to link Wikidata to the primary bioscience literature. We are really keen to integrate this with GeneWiki activities. The latest (Databases) paper is very impressive and echoes much of our thinking. This is just to reach out and make contact - we already know several of you. Marti Johnson is the WMF coordinator of the project and she was very keen for us to make contact. I think she will be coordinating meetups in the near future.
We've already prototyped the machine identification of genes in EuropePMC content and are optimistic of very useful precision-recall. We will shortly have a (probably weekly) trawl of EPMC Open Access content and we can work retrospectively later if required. Initially this could be bidirectional: "What Wikidata genes are in this paper?", and "what genes are in this paper that Wikidata might be interested in?" (possibly including a WikiCite addition). Petermr ( talk) 10:36, 11 November 2016 (UTC)
Hello Gene Wiki! In infoboxes of gene/protein articles, there are small thumbnail images of RNA expression pattern. I proposed switching these small thumbnail to full size image, because Wikipedia/Mediawiki image system was changed. Since image data are recalled from Wikidata, I post the proposal at Wikidata page ( wikidata:Property talk:P692#How about using full size image instead of small thumbnail?). I would like to get your thoughts on that. Thank you. -- Was a bee ( talk) 06:31, 18 March 2017 (UTC)
DPYD is the gene, and Dihydropyrimidine dehydrogenase is the enzyme. I keep forgetting if and how such pages should be merged. Thanks, ἀνυπόδητος ( talk) 15:41, 14 April 2017 (UTC)
![]() | This page is an archive of past discussions. Do not edit the contents of this page. If you wish to start a new discussion or revive an old one, please do so on the current talk page. |
Gene Wiki – Discussion |
Discussion moved from Talk:Mammalian target of rapamycin (see also Talk:BRCA1#Interactions):
The Interactions section has a huge number of references. Can we split the list (and references) into a separate mTOR interactions article or similar ? Rod57 ( talk) 18:26, 6 December 2010 (UTC)
{{
cite web}}
: Cite has empty unknown parameter: |coauthors=
(
help)I think the actual problem is the poor presentation of interactions as tediously long lists, and propose converting them to prose. See discussion at: talk:Converting interactions-sections to prose. Mikael Häggström ( talk) 07:00, 15 May 2011 (UTC)
An Error has occurred retrieving Wikidata item for infobox
This template causes this to appear:
But obviously it should instead have said this:
with an en-dash rather than a hyphen (see WP:MOS). As far as I can tell I can't edit this thing. Could whoever tends to this thing fix the punctuation error? Michael Hardy ( talk) 23:15, 12 February 2011 (UTC)
Could somebody sort out Complementarity determining region? Part of it was deleted some time ago (including refs), then it was expanded a bit, and I just can't sort out what is constructive and what not. Thanks, ἀνυπόδητος ( talk) 10:59, 13 February 2011 (UTC)
What is the best way to handle when one is referring to several isoforms of a gene. This came up in the FIG4 page where a link to yeast Atg18 was pointed to one of four mammalian WIPI proteins. For protein families, should a new page be generated? Davebridges ( talk) 22:57, 8 March 2011 (UTC)
PREP (gene) is a article completely bot-edited, it seems equivalent, but different from, Prolyl endopeptidase. Can some-one have a look at those two articles? -- Havang(nl) ( talk) 10:36, 12 March 2011 (UTC)
What is "A Proliferation Inducing Ligand (APRIL)" mentioned in B-cell activating factor and Belimumab, among other pages? HGNC knows two proteins with the synonym APRIL: ANP32B and TNFSF13. I suspect the latter, but could someone (i. e. most likely Boghog) confirm this? Thanks, ἀνυπόδητος ( talk) 19:53, 13 March 2011 (UTC)
A file that you uploaded or altered, File:PBB Protein MRPL11 image.jpg, has been listed at Wikipedia:Files 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. Thank you. Skier Dude ( talk) 03:04, 28 April 2011 (UTC)
A draft MCB Style Guide for gene/protein articles has been written. Since this style guide in principle applies to all Gene Wiki articles, I thought I should mention it here. Contributions and comments are welcome. Boghog ( talk) 20:23, 19 May 2011 (UTC)
There's a small escaping bug in the GeneWikiGenerator: "<" is shown as "& l t ;" (sans spaces), e.g. currently http://biogps.gnf.org/GeneWikiGenerator/#goto=genereport&id=29911 . MichaK ( talk) 15:54, 31 May 2011 (UTC)
Sorry to dig up an old issue, but I recently went through a bunch of gene/protein articles and changed the wording of all the lead sentences ( for example), not knowing that there was an agreed style for that first sentence. I think the problem was that it's not clear from the lead:
that the article is meant to address both the gene and the protein.
I think it would be a good idea to tweak this slightly to prevent another editor from coming through and making the same mistake. I was thinking maybe a hidden notice at the top of the page, like <!-- The lead sentence should be in the format:<recommended UniProt name> is a protein that in humans is encoded by the <approved HUGO gene symbol> gene.--> or adding a sentence at the top similar to a disambiguation notice, along the lines of "This article addresses both <protein> and <gene>. I don't know, though. Thoughts? Kerowyn Leave a note 06:33, 24 June 2011 (UTC)
Main subunit of cytochrome c oxidase states that COX1 and MT-CO1 contain this peptide. Does COX1 refer to PTGS1 here? Furthermore, COI (which is also a synonym of MT-CO1) links to a disambig and CO1 (??) to carbon monoxide which is rather unlikely to contain a polypeptide. Could someone clarify? Thanks -- ἀνυπόδητος ( talk) 06:45, 20 July 2011 (UTC)
(cross-post from the semi-active WP:WikiProject Cell Signaling) Any objections if I propose deletion of the signal transduction stub type? Category:Signal transduction stubs contains a rather arbitrary collection of 13 pages, most of which could go into Category:Receptor stubs or Category:Transmembrane receptor stubs. Thanks, ἀνυπόδητος ( talk) 17:15, 12 September 2011 (UTC)
It's come to my attention that ProteinBoxBot, which maintains this project's infoboxes, uses a curious template known as {{
PBB}} to add them to articles. For some reason this template insists on adding a wrapping table around the infobox and sticking an [edit] link above it, which not only pushes the infobox down articles but is also completely unnecessary as the infobox code supports an edit link anyway. ProteinBoxBot should instead be adding the name =
attribute to the infobox pages themselves. Adding | name = PBB/9353
to {{
PBB/9353}}, for instance, results in the output shown at {{
PBB/testcases}} (an unobtrusive link at the bottom of the template).
user talk:ProteinBoxBot redirects here, so if the ProteinBoxBot maintainers need any further details then please point them at my talk page. This is a trivial change which should positively impact the appearance and accessibility of thousands of articles.
Chris Cunningham (user:thumperward) - talk 19:58, 14 September 2011 (UTC)
{{{name}}}
parameter, I think you misunderstand its purpose: it is not the same as {{{Name}}}
(note the change in capitalisation) which gives the subject title, but in fact needs to refer to the current page title in order for the navbox magic to link to the correct view / talk / edit pages. Anyway, the first thing to do is to get ProteinBoxBot to add the links in question: once that's done, I'll update {{
PBB}} to take them into account. I've pinged the bot's owners with a link to this discussion.
Chris Cunningham (user:thumperward) -
talk 09:27, 15 September 2011 (UTC)PBB/9353
field, I'm a little hesitant to have both 'Name' and 'name' fields that do very different things. What if we put it under 'path' or 'PageLocation', or something similar? Boghog, I'm still not 100% sure I understand your suggestion regarding PAGENAME -- can you clarify? Cheers,
AndrewGNF (
talk) 16:38, 15 September 2011 (UTC) AndrewGNF: I agree that having both {{{name}}}
and {{{Name}}}
is confusing. If you want to go with {{{path}}}
for the parameter then I'll update {{
GNF_Protein_box}} to use that for the navbar links instead.
Chris Cunningham (user:thumperward) -
talk 06:10, 16 September 2011 (UTC)
{{{path}}}
parameter on its next run, which should be sometime in the next few days. I'll let
Chris know so he can change {{
GNF_Protein_box}} at that time.
Pleiotrope (
talk) 18:08, 16 September 2011 (UTC){{{path}}}
parameters and these are working fine, so I've updated {{
PBB}}. See the new, cleaner look on one of the new pages such as
TTLL3. Thanks, folks.
Chris Cunningham (user:thumperward) -
talk 11:41, 23 September 2011 (UTC)Albondin (gp60) is a sub-stub that might profit from a gene infobox. Or there already might be a gene article to which it could be merged. Thanks, as ever, ἀνυπόδητος ( talk) 08:08, 15 September 2011 (UTC)
Hello, I dropped a message with question here : http://en.wikipedia.org/wiki/Template_talk:GNF_Protein_box#IDs. Thanks :) Anthere ( talk) 07:12, 20 September 2011 (UTC)
The GeneWikiGenerator is down (504 Gateway Time-out). There has been a recent flurry of interest. Also is there any chance that the bugs first described here could be fixed? Thanks. Boghog ( talk) 17:15, 23 September 2011 (UTC)
We're soliciting feedback for the use of a new template that should be pretty useful on GeneWiki pages over at the village pump and we'd like your opinions. The example we use there is targeted to a broader audience, but we have some GeneWiki specific examples and motivation here: WP:Gene Wiki/SWL proposal. Thanks, Pleiotrope ( talk) 17:15, 19 October 2011 (UTC)
Since wikipedia is supposed to be useful to non-specialists, I went and added a whole bunch of wikilinks to DLX1: humans homeobox transcription factor Drosophila TGF-β craniofacial differentiation neurons forebrain chromosome 2 Alternatively spliced isoforms. Then I noticed that PBB updates the text and my wikilinks could get deleted pretty soon.
Is is worth adding some wikilinking ability to PBB so it can do this automatically to (the first appearance of) biology buzzwords? (Then you could get rid of the "require_manual_inspection" flag I added.)
I'm not quite sure what The Right Thing is here. Could PBB at least be changed to preserve the wikilink if the linked word is still in the replacement text? 71.41.210.146 ( talk) 16:56, 7 November 2011 (UTC)
A tag has been placed on Template:PBB/HP1BP3, requesting that it be speedily deleted from Wikipedia. This has been done for the following reason:
Under the criteria for speedy deletion, articles that do not meet basic Wikipedia criteria may be deleted at any time.
If you think that this notice was placed here in error, contest the deletion by clicking on the button labelled "Click here to contest this speedy deletion". Doing so will take you to the talk page where you will find a pre-formatted place for you to explain why you believe the page should not be deleted. You can also visit the page's talk page directly to give your reasons, but be aware that once tagged for speedy deletion, if the page meets the criterion, it may be deleted without delay. Please do not remove the speedy deletion tag yourself, but don't hesitate to add information to the page that would render it more in conformance with Wikipedia's policies and guidelines. If the page is deleted, you can contact one of these administrators to request that the administrator userfy the page or email a copy to you. Bulwersator ( talk) 08:40, 19 December 2011 (UTC)
Linked from / mentioned in a number of articles [1] [2]. NG2 is about a Puerto Rican Salsa duo which is probably unrelated. Anyone willing to write a bit about these? -- ἀνυπόδητος ( talk) 14:01, 20 December 2011 (UTC)
A file that you uploaded or altered, File:PBB Protein GSTA2 image.jpg, has been listed at Wikipedia:Possibly unfree files because its copyright status is unclear or disputed. If the file's copyright status cannot be verified, it may be deleted. You may find more information on the file description page. You are welcome to add comments to its entry at the discussion if you are interested in it not being deleted. Thank you. Stefan2 ( talk) 23:58, 16 January 2012 (UTC)
A file that you uploaded or altered, File:PBB Protein GSTA1 image.jpg, has been listed at Wikipedia:Possibly unfree files because its copyright status is unclear or disputed. If the file's copyright status cannot be verified, it may be deleted. You may find more information on the file description page. You are welcome to add comments to its entry at the discussion if you are interested in it not being deleted. Thank you. Stefan2 ( talk) 23:58, 16 January 2012 (UTC)
Further to the suggestion by BogHog that a discussion on my talk page (see here) would benefit from wider input, I'm bringing it here. In summary, I have started on a project to populate as many of the Gene Wiki pages as possible with "functional" information gleaned from model organisms. I guess the wider goal is to bring phenotypes to the Gene Wiki in as standardized a manner as possible. I think this is important, because much of the content we have on these genes are from various model organisms, and currently the information on the pages are a bit of a mishmash of references to mouse and human, and occasionally fly and yeast, orthologues. Orthologous genes do not necessarily share all the same characteristics between species, so there is a potential to mislead readers unless we are careful with these distinctions, and generally we haven't been.
So I have been creating "model organism" sections where that information, when present, can be sectioned off from the information on human genes. I have also been including new content pulled from the set of standarized mouse KO lines, generated by the International Knockout Mouse Consortium, and where available the standardized phenotypic analysis carried out on these animals by the various international phenotyping centres (accompanied by a collapsed summary table). A nice example of this is SLX4, though there are many more genes with much less interesting phenotypes (e.g. Ciliary neurotrophic factor receptor). There are currently around 500 genes with this information available in the mouse, and I plan to add them all to their Gene Wiki pages, and many more should be generated over the next few years. I should point out that I work at one of the phenotyping centres (The Wellcome Trust Sanger Institute). Though I am not directly involved the phenotyping project, I have been able to get the support of their informatics team. So I am starting with their data because I can generate it easily in a wiki-accessible format. It is my intention, however, to move on to the lines from the other centres (and try and convince them to provide me Wiki-friendly data dumps).
The bigger picture, of course, is to try and encourage the contribution of other model organism information for each gene, thereby increasing the knowledge base on Wikipedia. I'm content to continue adding these by hand over the coming months (and probably years) as I think there is value in a human parsing the information to identify the model organisms derived content, and then writing the section in a way that suits the article. However, there is also scope - as BogHog suggests - for bot assistance or merging some content to the infobox. I'm happy to defer to the consensus on that and any suggestions on how to proceed. But if there are no major objections to this, in the meantime I will continue to work on these one at a time. Rockpocke t 00:33, 27 January 2012 (UTC)
The message here pointed out some issues with the description of images uploaded by PDBbot, for example the previous description for Protein_CREBBP_PDB_1f81.png: "Structure of the CREBBP protein. Based on PyMOL rendering of PDB 1f81." The main issue is that PDB 1f81 corresponds to a fragment of the CREBBP protein, and a statement like "Structure of the CREBBP protein" could plausibly be interpreted to say that the image shows the entire protein. Also, there is nothing to indicate that 1f81 is from a mouse protein, and is not from a human -- here again, the omission of a detail could lead the reader to assume the image shows something it does not.
These issues potentially exist with many of the ~2,500 images uploaded by PDBbot. I updated the description of the image in question here; it now reads: "Structure of the TAZ2 domain (amino acids 1764-1850) of the CREBBP protein, as expressed in the common house mouse (Mus musculus). Based on PyMOL rendering of PDB 1f81". The information needed for that expanded description exists as structured data in the PDB entry for 1f81. I think most of the information needed for similarly expanded descriptions for all PDBbot images also exists in corresponding PDB files -- i.e., the range of residues depicted in the structure, the common and scientific name of the source organism.
Are there any issues with the revised description above? Does a description close to that form seem applicable to all PDB files? Thanks in advance for any feedback. Emw ( talk) 04:06, 13 March 2012 (UTC)
Hi! Concering the lead sentence in Gene Wiki articles, as discussed here and here, we have tried to make clear that these articles are not only about the human gene/protein, but also orthologs that exist in other species. The wording that was reached through consensus is perhaps a little awkward, but it is both accurate and concise:
I recently stumbled upon GLmol, which enables in-browser 3D manipulation of chemical structures as shown here, and was thinking to myself how neat it would be if something like that could be integrated into Wikipedia's protein infoboxes. GLmol use WebGL, a new web technology that puts OpenGL (the 3D engine used by PyMOL) into modern browsers. Ideas for using Jmol to do this have been brewing for a while (see here and here), but WebGL might be a worthwhile alternative to consider.
I see a few obstacles for implementing interactive WebGL-enabled PDB structures in Wikipedia infoboxes, along with possible solutions:
Does this seem like something worth pursuing? What are others' thoughts? Emw ( talk) 04:06, 13 March 2012 (UTC)
A prototype of this feature is available at http://pdbhandler.wmflabs.org. I've developed the feature as a MediaWiki media handling extension named "PDBHandler". It enables interactive 3D models of proteins and DNA on MediaWiki deployments like Wikipedia without the need for browser plug-ins. For browsers that don't support WebGL or have it enabled, a static image of the structure is shown instead of an interactive model. Some background that informed the development of the extension is in a discussion thread on the wikitech-l mailing list here.
Any feedback would be appreciated. I'll be working on this extension all day Tuesday and/or Wednesday at the hackathon in Wikimania 2012, so any input today or tomorrow is particularly welcome.
This feature loads 3D models only after the article's text and other media is ready and displayed on the user's browser, so users don't need to wait for the 3D model to finish loading to begin reading the article. In this sense, PDBHandler does not increase articles' page load time. To minimize the time needed to load and render the 3D models themselves, I've developed a custom compression scheme for PDB files that decreases their gzipped file size by roughly 30-70%.
The static images of structures shown for users that don't have WebGL enabled in their browser are identical to the kind produced by PDBbot. The static image is generated immediately after the PDB file's upload by modified PDBbot code that runs on a MediaWiki server. This approach doesn't have the disadvantage of relying on a remote third-party web service, and got favorable feedback from MediaWiki developers on IRC and the mailing list (e.g. here) relative to the remote-server approach.
An early prototype had a favorable user experience review from Wikimedia Foundation staff. It was decided that, for the extension's initial release to Wikipedia, interactive 3D models would an opt-in feature -- i.e., they would need to be manually enabled by users in their account preferences/'My preferences' page. The default behavior for the initial release, where users had not explicitly opted in, would be to show the static image representations of structures where an article had a PDB file wikilinked, e.g. [[File:1MBO.pdb]].
The feature has some loose ends, but I hope to mostly tie those up next week. I'll update here with news on the extension. Thanks in advance for any feedback on the prototype. Emw ( talk) 18:33, 8 July 2012 (UTC)
For {{ PBB/6790}}, several GO annotations appear multiple times in the list: e.g. centrosome, spindle, mitotic cell cycle. What's going on there? As an aside, how often are the GO annotations updated? MichaK ( talk) 10:36, 22 May 2012 (UTC)
There seems to be a major bug in the {{ PBB}} template. See, for example, CD20 -- the beginning of the article now reads: , {{{1}}}, {{{1}}}, Hide Hide, </a> </a>, , Membrane-spanning 4-domains, subfamily A, member 1 Rendering based on PDB 1S8B. Available structures PDB Ortholog search: PDBe, RCSB , {{{1}}}, {{{1}}}, {{{1}}}, {{{1}}}, {{{1}}}, , {{{1}}}, {{{1}}}, {{{1}}}, {{{1}}}, {{{1}}}, MyPDB MyPDB, , {{{1}}}, {{{1}}}, Hide Hide, </a> </a>, , [show]List of PDB id codes , , , {{{1}}}, {{{1}}}, {{{1}}}, {{{1}}}, {{{1}}}, {{{1}}}, {{{1}}}, {{{1}}}, {{{1}}}, , {{{1}}}, , {{{1}}}, Username: Username: , {{{1}}}, Password: Password: ...etc., etc. Pjbradle ( talk) 16:42, 30 May 2012 (UTC)
I am in contact with the National Center for Biotechnology Information (who run web services like PubMed Central) over them providing references in a way that allows for easy copy-pasting into Wikipedia articles (similar to what Europeana does or the Biomedical citation maker). Where would be the best place to discuss what Wikipedia template formats (e.g. {{ Cite web}}, {{ Cite journal}}, {{ Citation}}, {{ Cite book}}) would be best to implement at what NCBI projects? Thanks for any pointers. Please reply at WikiProject NIH.
Another point of interest is how NCBI content could be used to update infoboxes (or even article text), similar to what PBB does - what is the best place to discuss such matters? -- Daniel Mietchen - WiR/OS ( talk) 04:00, 18 July 2012 (UTC)
Hi. I saw this Nature Communications article (as widely reported), and so searched for MIR941-1, which was created today - that article has some sort of a {{ PBB}} problem at the top, (maybe just a remnant that the bot is leaving behind?) and too much whitespace under the intro-sentence - both should probably be fixed at the source-level. This is mostly just a note for the bot maintainer ( User talk:ProteinBoxBot redirects to here), but also a pointer towards interesting articles (both ours and Nature's). HTH. — Quiddity ( talk) 18:59, 23 November 2012 (UTC)
A bot request to create systematic redirects for Gene Wiki articles so that they are easier to located has been submitted here. Comments and suggestions are welcome. Boghog ( talk) 05:02, 2 January 2013 (UTC)
it's not working for ARGLU1. the gene id is correct, so no clue as to what's happening. regards, FoCuSandLeArN ( talk) 13:51, 5 February 2013 (UTC)
Similar problem over at C9orf16 (gene). Brightgalrs (/braɪtˈɡæl.ərˌɛs/) [1] 17:28, 17 May 2013 (UTC)
Another ATXN7L2 (gene) Brightgalrs (/braɪtˈɡæl.ərˌɛs/) [1] 01:25, 8 June 2013 (UTC)
Having just discovered this portal, it seems like it belongs in the Project namespace. According to WP:Portal, "The idea of a portal is to help readers and/or editors navigate their way through Wikipedia topic areas through pages similar to the Main Page." This page seems to be more of a WikiProject. -- Ypnypn ( talk) 15:19, 26 May 2013 (UTC)
Gang -- Look at this page as an example: /info/en/?search=Ubiquitin#Human_proteins_containing_ubiquitin_domain In that section "Human proteins containing ubiquitin domain" I would like to link to wikigenes.org for the genes that do not have wikipedia pages. For example, UBL7 has no wikipedia page but does have a page here: http://www.wikigenes.org/e/gene/e/84993.html
Is the goal to link to wikigenes.org? Or some other gene wiki? How to do so in wiki code? JesseAlanGordon ( talk) 14:59, 9 July 2013 (UTC) Jesse Gordon, July 9, 2013
If you have ideas or suggestions as to which data NCBI should make available about traffic they get from Wikimedia servers, please list them here. Thanks! -- Daniel Mietchen ( talk) 21:21, 25 October 2013 (UTC)
Article AAVS1 (gene) was recently created by User:ProteinBoxBot and it includes two templates that don't exist: Template:PBB/17 and Template:Gene-17-stub. -- Derek Andrews ( talk) 01:51, 11 November 2013 (UTC)
The BioGPS for generating new Gene Wiki articles has been down some time. There are still ~10,000 gene to go. :-) Boghog ( talk) 07:45, 11 November 2013 (UTC)
Hi. ProteinBoxBot is making a large number updates that seem to be in error. See for example diff. Regards Boghog ( talk) 10:42, 15 November 2013 (UTC)
This change has been corrected. Uniprot had a misconfigured mirror which accounted for the request bodies being injected in their response. I updated our bot to fix the incorrect pages that were introduced and all seems back to normal. Cheers x0xMaximus ( talk) 21:39, 16 November 2013 (UTC)
This is mentioned in Pirinixic acid. Is this the same as PNPLA2, as the link in Serine hydrolase suggests? -- ἀνυπόδητος ( talk) 12:28, 25 November 2013 (UTC)
In the course of editing underlinked articles, I've discovered that the PBB template for HMGCS2 isn't working, and I don't know how to fix it...thought I should let you know. WQUlrich ( talk) 00:25, 26 November 2013 (UTC)
Is this also encoded by DRD2? If yes, should it be merged to Dopamine receptor D2? If no, should it have an infobox? -- ἀνυπόδητος ( talk) 08:40, 9 February 2014 (UTC)
Well, they are redirected, but it would be quicker and cause less traffic if the URL http://www.informatics.jax.org/searches/accession_report.cgi?id=MGI:{{{1}}} in {{ MGI}} were changed to http://www.informatics.jax.org/marker/MGI:{{{1}}}. I haven't found evidence that this is true for all pages, and given the high visiblity of the template, I'd rather leave the change to somebody else, i.e. Boghog. -- ἀνυπόδητος ( talk) 08:40, 9 February 2014 (UTC)
This article's trying to transclude a non-existent template (that doesn't seem to have been deleted previously, so maybe it never existed?), but it's not some sort of vandalism or accidental on-page breakage (no edits since shortly after the bot created it). Facing the Sky ( talk) 16:36, 1 March 2014 (UTC)
I can't find anything about this cytokine(?). The refs are about macrophage migration inhibitory factor and platelet activating factor as far as I can see. -- ἀνυπόδητος ( talk) 19:46, 2 December 2014 (UTC)
CACNA2D3 and CAMK1D both contain nonexistent subtemplates of Template:PBB. I can see how I would create those subpages using Template:GNF Protein box, but if ProteinBoxBot can instead that would be even better.— Neil P. Quinn ( talk) 17:33, 11 January 2015 (UTC)
For several weeks now, the BioGPS GeneWikiGenerator has not been able to create Wikipedia pages (failed creating both PBB template and GeneWiki article, Status: creation failed). One could manually create the pages by copy and pasting the output of GeneWikiGenerator into Wikipedia. Can someone take a look at this? Thanks. Boghog ( talk) 08:08, 3 April 2015 (UTC)
I am not sure where to post this request, but I saw on the Ideas Page that additional links are planned in the future for the protein box. I wanted to ask if there was a possibility to add another source to this list. Specifically I would like to suggest Genevisible which is a free resource for finding the top 5 expressing tissues/cancers/perturbations for a given gene. I will be honest here and state that I am one of the maintainers of that resource and am willing to help get a dynamic plot working (something akin to the GeneAtlas plots already in the protein box) should there be interest for it. However, I would already be grateful if a direct link from a protein/gene page to its relevant entry on our resource was added to the protein box. Here is an example for HP1BP3. I am ready to answer any questions you might have regarding this and would gladly help in implementing/testing the feature should it be accepted. Ovoggen ( talk) 11:45, 30 July 2015 (UTC)
Hi! Just wanted to note that PSMA8 is the only one of the {{ Proteasome subunits}} that hasn't got an article. -- ἀνυπόδητος ( talk) 08:50, 18 October 2015 (UTC)
Hi, what do i have to do to get parts of the reviewed items from UniprotKB (accession number, protein name, gene name, organism, GO - molecular and biological function, keywords, length, mass and sequence) into wikidata? A lady at UniprotKB told me that you already have their permission. Please see the discussion there, all the best, -- Ghilt ( talk) 21:59, 9 May 2016 (UTC)
Hi,
I would like to import drug-protein (drug-target, drug-enzyme, etc) interactions to gene_wiki from DrugBank. Would the gene_wiki community be interested in this, and, if so, what is the best way to import this data.
Thank you for your help.
Crowegian ( talk) 04:33, 24 May 2016 (UTC)
C11orf52 is an orphaned protein/gene article without an infobox. Thanks as always, Boghog! -- ἀνυπόδητος ( talk) 09:49, 10 September 2016 (UTC)
We are delighted that we have been awarded a WMF grant for WikiFactMine - a project to link Wikidata to the primary bioscience literature. We are really keen to integrate this with GeneWiki activities. The latest (Databases) paper is very impressive and echoes much of our thinking. This is just to reach out and make contact - we already know several of you. Marti Johnson is the WMF coordinator of the project and she was very keen for us to make contact. I think she will be coordinating meetups in the near future.
We've already prototyped the machine identification of genes in EuropePMC content and are optimistic of very useful precision-recall. We will shortly have a (probably weekly) trawl of EPMC Open Access content and we can work retrospectively later if required. Initially this could be bidirectional: "What Wikidata genes are in this paper?", and "what genes are in this paper that Wikidata might be interested in?" (possibly including a WikiCite addition). Petermr ( talk) 10:36, 11 November 2016 (UTC)
Hello Gene Wiki! In infoboxes of gene/protein articles, there are small thumbnail images of RNA expression pattern. I proposed switching these small thumbnail to full size image, because Wikipedia/Mediawiki image system was changed. Since image data are recalled from Wikidata, I post the proposal at Wikidata page ( wikidata:Property talk:P692#How about using full size image instead of small thumbnail?). I would like to get your thoughts on that. Thank you. -- Was a bee ( talk) 06:31, 18 March 2017 (UTC)
DPYD is the gene, and Dihydropyrimidine dehydrogenase is the enzyme. I keep forgetting if and how such pages should be merged. Thanks, ἀνυπόδητος ( talk) 15:41, 14 April 2017 (UTC)