Module talk:Infobox gene

Image error in sandbox

There is a subtle image error that was introduced in recent sandbox edits. An example from the testcases page, {{#invoke:Infobox_gene/sandbox|getTemplateData|QID=Q2035393}}, renders [[File:Human chromosome 5 ideogram.svg|300px|Chromosome 5 (human)|5 (human)]]. Note the extra file caption, which causes the page to appear on error reports. Please fix this error in the sandbox code. (The live module renders [[File:Ideogram human chromosome 5.svg|300px|Chromosome 5 (human)]], which is fine.) – Jonesey95 (talk) 21:58, 7 October 2024 (UTC)

Reverted pending a response, to clear these image errors from Template space. Feel free to reinstate the changes for testing, as long as they get fixed. Check "Page information" for {{Infobox gene/testcases}} to see if the Linter errors return. – Jonesey95 (talk) 00:24, 10 October 2024 (UTC)

The invalid changes have been restored by Jmarchn without an edit summary or a comment here. Please fix these errors. – Jonesey95 (talk) 14:47, 19 October 2024 (UTC)

I have commented out the bit of code that appears to have been causing this problem. Please do not restore it without fixing the image errors. Please use edit summaries. – Jonesey95 (talk) 05:17, 22 October 2024 (UTC)

@Jonesey95: Sorry for the delay in replying. I didn't see your comments initially. Then I fixed the bugs (that you pointed out to me) at the same time as I improved the code, integrating lines of code that were almost repetitive into new functions.

I have introduced new messages for chromosome images (Ideogram human chromosome %s.svg and Ideogram of house mouse chromosome %s.svg). As you must have seen, the text is located in Module:Infobox gene/sandbox/en. They are named HumanChromosomeIdeogr and MouseChromosomeIdeogr. I don't know if the text of these messages should be modified, as my level of English is not very good. Maybe it would be better "Human/Mouse chromosomes and mitochondrion, framed: %s". What do you think about this?

We have a new problem: PubMed addresses are no longer valid. Maybe you know how to fix it, otherwise the PubMed row should be hidden or deleted.

I guess you must have noticed by now that it is ready for right-to-left writing languages. You can see how it works at ar:وحدة:Infobox gene/sandbox.

Currently this module already work in the Catalan and Basque wikipedia.

Waiting for your answer and to enable to go from sandbox to final version.

The current sandbox code does not have any syntax errors. I have not examined {{Infobox gene/testcases}} for other errors, though I do see some differences. – Jonesey95 (talk) 14:54, 29 October 2024 (UTC)

@Jonesey95: Fixed two bugs ("Orthologs" without link and "RefSeq (protein)" list without collapse). Also I change the InfoboxFontSize from 90 to 85%. Jmarchn (talk) 17:41, 29 October 2024 (UTC)

@Jmarchn are you planning to pursue this? Gonnym (talk) 12:50, 22 December 2025 (UTC)

@Jonesey95 and Synpath: Follow what? I had made an easily translatable version, which is used in several wikis, and Synpath, without warning me, belittles my work. It seems that the fact that a template is easily translatable to other Wikipedias does not interest those who speak and work on the English Wikipedia. I think the normal thing would have been to modify the version that I made. Jmarchn (talk) 06:49, 28 December 2025 (UTC)

I don't think I participated in this discussion, and I don't wake up in the morning looking to put people down. So, I'm confused about the context, can you bring me up to speed? ⇌ Synpath 14:05, 28 December 2025 (UTC)

Edit request 24 October 2025

@Tarsmf: I noticed that you replaced the link from the now-defunct HomoloGene to the Orthologous MAtrix (OMA) browser, which I greatly appreciate. However, I would like to discuss an alternative, the NCBI Gene database, which now includes an “Orthologs” tab (see HomoloGene Now Redirects). For comparison, here are the ortholog entries for TP53:

• https://omabrowser.org/oma/vps/ENSG00000141510/ (linked via Ensembl ID)
• https://www.ncbi.nlm.nih.gov/datasets/gene/7157/#orthologs (linked via Entrez ID)

The OMA page currently takes a long time to load and displays only 25 of the 148 available orthologs in its database, even after reloading. In contrast, the NCBI Orthologs database loads quickly, lists all 552 orthologs, and provides more detailed information overall. Would you mind if we changed the link to the NCBI Orthologs page instead? Boghog (talk) 07:27, 24 October 2025 (UTC)

Update: Now OMA is downloading data much faster and displays all of the available records. However there is still the issue that NCBI Orthologs database appears more complete (552 vs 148 orthologs for TP53) and contains more information overall. Boghog (talk) 10:13, 24 October 2025 (UTC)

Not done for now—Not clear from later comment if this is still required. Andy Mabbett (Pigsonthewing); Talk to Andy; Andy's edits 17:23, 8 December 2025 (UTC)

Unknown params

Was going to add Module:Check for unknown parameters to the Template version of this... It looks like the ONLY parameter it accepts is |QID=, can anyone confirm this? Zackmann (^{Talk to me}/_{What I been doing}) 23:50, 30 October 2025 (UTC)

Yep, Infobox gene is meant to get all of its information from Wikidata. The qualifier ID field is only used when putting the box onto a page of a different gene/protein/other topic, and you have to invoke the module directly to do so. ⇌ Synpath 01:19, 31 October 2025 (UTC)

awesome! Thanks much! Zackmann (^{Talk to me}/_{What I been doing}) 02:07, 31 October 2025 (UTC)

Edit request 11 June 2026

Description of suggested change: Addition of a parameter that can collapse the orthologs section by default, to use on some pages where the space it takes up causes images to be misplaced unless the section is hidden. Proposed change has been made in the sandbox, with the parameter named "collapse_orthologs" Diff:

−

local mm_qid = ""

+

"local mm_qid = "" local collapse_orthologs = mw.text.trim(frame.args['collapse_orthologs'] or '')

Full diff: nahle.ghini (talk) 06:41, 11 June 2026 (UTC)

MOS:COLLAPSE suggests not collapsing information by default. Can you please link to a couple of pages where this problem exists? – Jonesey95 (talk) 14:44, 11 June 2026 (UTC)

This would not be a change to the usual template, just a parameter that can be applied to a few pages such as Activity-regulated cytoskeleton-associated protein, where the thumb images for different sections are misaligned by default when opening the page, which is then fixed by hiding Orthologs on the template. nahle.ghini (talk) 18:46, 11 June 2026 (UTC)

I see what you are talking about. Thanks for the link. I don't have enough knowledge of this template's contents to know whether the information in the "Orthologs" section is important enough to be shown or collapsed by default; this may be a significant change to the template that others may object to. It would be helpful to get more opinions to see whether there is consensus for this change. – Jonesey95 (talk) 14:52, 13 June 2026 (UTC)