Template talk:Infobox gene/Archive 1

Archive 1

Missing information on RNA expression pattern

At the time of writing this there is no article on Wikipedia describing exactly what a "RNA expression pattern" is, and how to read it. Please, can someone more knowledgeable than me (or rather much more knowledgeable) start an article? Tony Mach (talk) 15:52, 10 November 2016 (UTC)

I think Gene expression profiling (i.e., the measurement of an expression pattern) comes pretty close. Perhaps a redirect to this article would be sufficient. Boghog (talk) 18:33, 10 November 2016 (UTC)

I was thinking along similar lines -- but just hyperlinked the header to gene expression (diff). Gene expression profiling would be just fine by me too... Also @Tony Mach:, if you click on the thumbnail and then on the "more details" link, you will get to a page (eg File:PBB_GE_SLC2A1_201249_at_tn.png) that also shows the larger version of the image. That might make a bit more sense because it has tissue and cell types shown across the bottom... Best, Andrew Su (talk) 05:18, 11 November 2016 (UTC)

@Boghog Is a RNA expression pattern the result of gene expression profiling? This was not clear to me! I suspected that these are similar, if not the same. But how exactly are they related? If there is a relation between the two, then somebody please put a short paragraph there in that article. Then link to it from the template, that would be wonderful. @Andrew Su:: Yes, I did see that, yet there was no explanation on wikipedia on what exactly this RNA expression pattern is – here on wikipedia it is just a colorful image with no explanation what it is and no help how to read. I had a hunch what it probably is – but my hunches can be wrong and I wanted a more reasoned explanation than "I guess that's what it is" (others might need too!), hence my request for an explanation somewhere on wikipedia. (As an example, see the article on "Western blot" – though while the "Western blot" article explains what it is and how it's made, it is sadly a bit light on how a Western blot is interpreted...) Tony Mach (talk) 06:43, 11 November 2016 (UTC)

Confusing layout/display of wikidata section

"Wikidata" appears as a gray-backround full-width bar, indicating that what comes next is a section of links to wikidata. What actually comes next, for example, "View/Edit Human" in Calmodulin 1, is also gray-background, which makes it seem to be a new section heading rather than a sub-item under the wikidata heading. From reading the Module:Infobox_gene, the only possible entries in the wikidata section are human and mouse, so maybe this section could be formatted as a two-column table of species-name and "view/edit" links. Or else "wikidata" could become another row in the preceding "Orthologs" section, where there are already separate columns for each species. DMacks (talk) 21:06, 10 December 2016 (UTC)

Categorisation in userspace

This template adds a category such as Category:Genes on human chromosome 3 even to draft articles in userspace, which should not be happening per WP:USERNOCAT. This could be avoided by putting the category in a {{Main other}} template or similar - I won't do it myself as I get nervous around big templates...<g> Le Deluge (talk) 13:29, 14 December 2016 (UTC)

Documentation lacking

The documentation needs to include info on how to edit information in the infobox via subpages of {{PBB}}. E.g. if a used needs to add an additional alias of a protein. T.Shafee(Evo&Evo)^talk 01:59, 21 March 2017 (UTC)

EC numbers not rendered

The IMHO, Enzyme Commission numbers (EC enzyme number (P591)) are pretty important and were displayed in the old GNF Protein Box. However this data apparently has not been systematically migrated to Wikidata. Furthermore, even if this data is manually added to Wikidata (e.g., see this edit), it is not render in the infobox (see Protein C). Looking in the code in Module:Infobox gene, there is a variable called ec_no, so I do not understand why this data is not displayed. I would really appreciate if someone would take a look at this. Thanks. Boghog (talk) 05:33, 4 June 2017 (UTC)

Gene location column added to infobox gene at Module page

New column which shows gene location is added to infobox gene. Feedback welcome at Module talk:Infobox gene#Gene location column added. Thanks! --Was a bee (talk) 12:17, 18 August 2017 (UTC)

Wikidata link

At the bottom of this infobox (e.g. at Factor XII), there is a link called "Wikidata", which leads to Wikidata. This is useless: either the link should be to the exact page where the information in the infobox comes from, or the link should go (or at the very least, but still highly insufficient, be changed to "data taken from Wikidata" or something similar). As it stands, this is a link which has no value for our readers at all (why is this infobox linked to the article Wikidata? No idea) and is no help for our editors. Fram (talk) 14:27, 19 September 2017 (UTC)

The Wikidata internal link is a header which explains what type of external links are below it:

• Wikidata
  • View/Edit Human
  • View/Edit Mouse

This structure is identical to the rest of the links in the infobox (explanatory internal link followed by an external link). Boghog (talk) 15:33, 19 September 2017 (UTC)

Not at all clear though. The others are an explanation of what value you get shown, then the value, and then the reference. Here, you get a word (Wikidata) with no meaning (for the infobox), no value, and then in a separate box below it (separated by a white line, not connected visually to "Wikidata" at all) two edit links. I suppose you compare it to what you get in the Orthologs box above it, but these are displayed visually completely different. As it stands, I would suggest to either display the Wikidata plus two edit links in the same way (Wikidata left, two links right of it), or to omit the "Wikidata" text and just have "View/Edit human" and "View/Edit mouse" or something similar. Please try to look at the infobox with the eyes of a reader or editor without the knowledge you already have, and compare the layout and meaning of the different elements. Fram (talk) 17:58, 19 September 2017 (UTC)

Added "Data structure" section to documentation

I added "Data structure" section to the documentation page (diff). First reason is that there was no information about this. Second reason is that this data structure can be interesting model for various Wikipedia/Wikidata editors in other fields. P.S. My English may be wrong or unnatural. If you noticed something, please correct it. Sorry and thank you. --Was a bee (talk) 13:45, 23 November 2017 (UTC)

Merging Wiki Data items

GBE1 has been merged into Glycogen branching enzyme (seems reasonable since there is only one human gene encoding a glycogen branching enzyme). I wanted to merge GBE1 (Q18025526) into 1,4-alpha-glucan branching enzyme 1 (Q161537) but I am not sure how to do this. If anyone could give me some pointers, I would appreciate it.

Also while we are at it, 1,4-alpha-glucan branching enzyme 1 should be merged into Glycogen branching enzyme.

Boghog (talk) 14:07, 13 April 2018 (UTC)

Hello @Boghog:. Here is How to (d:Help:Merge). --Was a bee (talk) 16:55, 13 April 2018 (UTC)

Thanks for the tip. The special merge page did not work, but the gadget did finally work. Boghog (talk) 08:48, 14 April 2018 (UTC)

Categorization w.r.t. Wikidata

Maybe one should add Category:Articles with infoboxes completely from Wikidata. Wikisaurus (talk) 01:32, 6 October 2018 (UTC)

Wide

Don't forget to </br> long strings to keep from producing wide templates. Currently the Ensembl numbers are two or three glyphs long (to reduce the template an ideal 1/2 width) at my screen font size, which is normal readable for electronic display screens: browser font size 16, Windows size slider 100% (normal). -Inowen (nlfte) 20:49, 30 November 2018 (UTC)

Template-protected edit request on 30 March 2019

I have relisted the TfD discussion - please change che March 20 link to March 30. Thanks, --DannyS712 (talk) 16:44, 30 March 2019 (UTC)

@DannyS712: Am I missing something, I do not see this template listed on the March 30 page. - FlightTime (open channel) 16:55, 30 March 2019 (UTC)

@FlightTime: Its part of Wikipedia:Templates for discussion/Log/2019 March 30#Template:GNF Protein box --DannyS712 (talk) 16:56, 30 March 2019 (UTC)

AH, OK doing. - FlightTime (open channel) 16:57, 30 March 2019 (UTC)

 Done - FlightTime (open channel) 16:59, 30 March 2019 (UTC)

Deleted?

@Jo-Jo Eumerus: If Template:GNF Protein box is being merged into this template, why did you tag this page with {{being deleted}}? I hope you aren't planning to cut the backlinks to this page. Seppi333 (Insert 2¢) 18:49, 20 May 2019 (UTC)

No, that was just a screw-up; I've remedied it. Jo-Jo Eumerus (talk, contributions) 18:52, 20 May 2019 (UTC)

Ah, ok. Thanks. Seppi333 (Insert 2¢) 18:53, 20 May 2019 (UTC)

Outdated links to HGNC in Infobox

The "Aliases" field in Infobox Gene contains the approved HGNC symbol as the first entry, with the link in a very outdated format eg https://www.genenames.org/cgi-bin/gene_symbol_report?hgnc_id=7565 , the correct link should be in the format https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/7565 . I cannot identify the provenance of these URLs and so haven't been able to update them myself. The URL formats for HGNC ID and HGNC Symbol in WikiData are correct, and I can't access the source for the Template:Infobox gene, so I don't know where this comes from. If this URL format is specified in the Template can it please be updated? Aretaon (talk) 15:46, 5 December 2019 (UTC)

I realized the correct place to make this request was on the "Module talk:Infobox gene" page so I have now done this. Aretaon (talk) 10:20, 16 December 2019 (UTC)

Gene ontology list

Hello, currently the list under the "Gene ontology" section, which starts with "peptidyl-dipeptidase activity", is not a proper list. Please convert it to improve semantics and accessibility. Thank you. Opencooper (talk) 20:45, 2 June 2020 (UTC)

Template-protected edit request on 5 January 2021

This template generates a missing end tag lint error for italics (''). I went to Special:ExpandTemplates, with the context title set to "PPP2R3A" and with the Input wikitext consisting only of {{Infobox gene}}, shows the offending markup is in the markup for this table cell:

<td colspan="3" style="background:#eee"><span class="plainlinks">[https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/9307 PPP2R3A]</span>, PPP2R3, PR130, PR72, protein phosphatase 2 regulatory subunit B''alpha</td>

Obviously what's needed is a closing '' just before </td>. This is just one example and I have no idea how this all works, so it's possible that the module needs more than one change to accomplish the fix for all possible cases. — Anomalocaris (talk) 05:16, 5 January 2021 (UTC)

 Not done: it's not clear what changes you want to be made. Please mention the specific changes in a "change X to Y" format and provide a reliable source if appropriate. DannyS712 (talk) 03:11, 7 January 2021 (UTC)

Template-protected edit request on 9 February 2022

This template generates a lint error (missing italics end tag) for several articles, including PPP2R3A, BDP1, and PPP2R3C. Judging from the above thread, the template has had lint errors for more than a year. 🐔dat (talk) 11:43, 9 February 2022 (UTC)

Gnarly challenge. 🐔dat, I looked at the Linter list for mainspace and found that the missing end tag error is caused by several different infoboxes on different article pages. How do we tell if it's Infobox gene or if it's the main Infobox used to generate the more specific iboxes? If the problem is in the {{Infobox}} template, fixing it could erase a good many errors in the Linter list. As for the table error in the previous discussion, that appears to have been fixed by converting to Lua, since I cannot find that code in Module:Infobox gene. Curious situation, and while there are presently over 5 million pages with the "missing end tag" error (a low priority Linter error) it's still worth pursuing imho. P.I. Ellsworth - ed. ^put'r there 21:30, 9 February 2022 (UTC)

I may have the answer. PPP2R3A is in the B''alpha family, but in one place in the infobox (the Aliases column), they forgot to put the nowiki tags in, so it shows as Balpha. (except without the closing italics tag) However, I'm not sure how to change that, since the code for the visual rendering is somewhere else. 🐔dat (talk) 11:03, 10 February 2022 (UTC)

PPP2R3A just disappeared from Special:LintErrors. 🐔dat (talk) 11:42, 10 February 2022 (UTC)

I already addressed this question at the Module talk page. I'm not sure why Chicdat is posting this problem again and did not ping me. – Jonesey95 (talk) 14:59, 10 February 2022 (UTC)

Well, the lint error did get fixed this time. 🐔dat (talk) 10:53, 11 February 2022 (UTC)