Module talk:Infobox gene
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![]() | Infoboxes | |||
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Request to add Expression Atlas links
Initial disclaimer: I am the Lead Developer of Expression Atlas and Single Cell Expression Atlas web applications (https://www.ebi.ac.uk/people/person/alfonso-munoz-pomer-fuentes/).
A couple of years ago a proposal to add Expression Atlas to the infobox was briefly discussed. I’d like to bring the topic back, and gauge how much interest there is in the community. I’ve been hacking around the Lua code and I got to add three useful links for a given gene: bulk baseline expression (e.g. mRNA-seq experiments), bulk differential expression (e.g. microarray experiments) and single-cell expression (single cell RNA-seq).
See an example below. Feel free to offer any suggestions. I’m not very knowledgeable in Lua, but I tried to follow the conventions I saw in the module.
File:Infobox gene (sandbox) with Expression Atlas links.png – Alfonso Muñoz-Pomer Fuentes (talk) 16:44, 4 August 2022 (UTC)
Template-protected edit request on 2 March 2023
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Error: [778:86] invalid escape sequence near '\:' مهدی بهرامی مطلق (talk) 16:29, 2 March 2023 (UTC)
- Not sure where you saw this error, but I believe \: and \; are not required, please check diff — Martin (MSGJ · talk) 21:51, 3 March 2023 (UTC)
- That was a massive and very productive edit! I didn't check all the details but it looked good and fixed the reported problem. Johnuniq (talk) 01:10, 4 March 2023 (UTC)
- Had my Lua-challenged mind puzzled! Seems that the error is found in the [edit screen]. Click on the red x-box at the bottom of the edit screen to actually see the error. That does not appear in the sandbox's edit screen. P.I. Ellsworth , ed. put'er there 07:42, 4 March 2023 (UTC)
Human UniProt search error
I am not sure if this is a problem in Infobox gene or Wikidata, but the rendering of the Human UniProt search link in Mucin-1 is not right. Does anyone have any idea how to fix this? Thanks. Boghog (talk) 06:43, 26 April 2023 (UTC)
Done The problem was in Wikidata. Only one UniProt ID should be associated with the human protein, not two. Fixed in this edit. Boghog (talk) 06:50, 26 April 2023 (UTC)
Edit request 15 January 2024
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Modify Bgee links
The Bgee links changed. To avoid redirections, please include "www" in the URLs as shown below. Thank you very much for your help.
Diff:
− | local bgee_gene_page = "https: | + | local bgee_gene_page = "https://www.bgee.org/gene/" |
− | bgee_title = "[https: | + | bgee_title = "[https://www.bgee.org/ " .. bgee_title .. "]" |
Tarsmf (talk) 16:21, 15 January 2024 (UTC)
Done. Tested at FOXS1. – Jonesey95 (talk) 00:27, 16 January 2024 (UTC)
Edit request 22 May 2024
![]() | It is requested that an edit be made to the template-protected module at Module:Infobox gene. (edit · history · last · links · sandbox · edit sandbox · sandbox history · sandbox last edit · sandbox diff · test cases · transclusion count · protection log) This template must be followed by a complete and specific description of the request, so that an editor unfamiliar with the subject matter could complete the requested edit immediately.
Edit requests to template-protected pages should only be used for edits that are either uncontroversial or supported by consensus. If the proposed edit might be controversial, discuss it on the protected page's talk page before using this template. Consider making changes first to the module's sandbox and test them thoroughly here before submitting an edit request. To request that a page be protected or unprotected, make a protection request. When the request has been completed or denied, please add the |
Description of suggested change:
Improve External IDs readability. In the 'Identifiers tab, external IDs are difficult to read because there is no semicolon separating them. The code below adds semicolons between IDs. In addition, it also adds another external ID of the OMA database that is complementary to HomoloGene with richer information about homologous genes. It was tested here: Module_talk:Infobox_gene/testcases. Thank you very much for your help!
Diff:
Suggestion to add this trim function (to remove empty spaces) in line 23 or in any place on top of the code:
− | + | local function trim(s)
return (s:gsub("^%s*(.-)%s*$", "%1"))
end |
Line 196
− | p.renderIdentifiers(aliases, hgnc_id, gene_symbol, homologene_id, omim_id, mgi_id, ChEMBL_id, IUPHAR_id, ec_no, | + | p.renderIdentifiers(aliases, hgnc_id, gene_symbol, homologene_id, omim_id, mgi_id, ChEMBL_id, IUPHAR_id, ec_no, entrez_gene, ensembl) |
Line 399
− | function p.renderIdentifiers(aliases, hgnc_id, gene_symbol, homologene_id, omim_id, mgi_id, ChEMBL_id, IUPHAR_id, ec_no, | + | function p.renderIdentifiers(aliases, hgnc_id, gene_symbol, homologene_id, omim_id, mgi_id, ChEMBL_id, IUPHAR_id, ec_no, entrez_gene, ensembl) |
Line 433
− | omim = | + | omim = trim(string.gsub(omim, ", $","")) --remove comma from end
if (omim ~= "") then omim = omim.."; " end |
Line 446
− | homolo = | + | homolo = trim(string.gsub(homolo, ", $","")) --remove comma from end
if (homolo ~= "") then homolo = homolo.."; " end |
− | genecards = genecards.."[https://www.genecards.org/cgi-bin/carddisp.pl?gene="..gene_symbol.." "..gene_symbol.. | + | genecards = genecards.."[https://www.genecards.org/cgi-bin/carddisp.pl?gene="..gene_symbol.." "..gene_symbol.."]; " |
Line 463
− | mgi = | + | mgi = trim(string.gsub(mgi, ", $","")) --remove comma from end
if (mgi ~= "") then mgi = mgi.."; " end |
− | ChEMBL = "[[ChEMBL]]"..": ".."[https://www.ebi.ac.uk/chembldb/index.php/target/inspect/CHEMBL"..ChEMBL_id.." "..ChEMBL_id.. | + | ChEMBL = "[[ChEMBL]]"..": ".."[https://www.ebi.ac.uk/chembldb/index.php/target/inspect/CHEMBL"..ChEMBL_id.." "..ChEMBL_id.."]; " |
− | IUPHAR = "[[International_Union_of_Basic_and_Clinical_Pharmacology|IUPHAR]]"..": ".."[http://www.guidetopharmacology.org/GRAC/ObjectDisplayForward?objectId="..IUPHAR_id.." "..IUPHAR_id.. | + | IUPHAR = "[[International_Union_of_Basic_and_Clinical_Pharmacology|IUPHAR]]"..": ".."[http://www.guidetopharmacology.org/GRAC/ObjectDisplayForward?objectId="..IUPHAR_id.." "..IUPHAR_id.."]; " --**lclz** |
Line 478
− | local EC = "[https://www.genome.jp/dbget-bin/www_bget?enzyme+" .. link_ec_no .. " " .. ec_no .. | + | local EC = "[https://www.genome.jp/dbget-bin/www_bget?enzyme+" .. link_ec_no .. " " .. ec_no .. "]; "
local oma = "[[Orthologous_MAtrix|OMA]]"..":"
oma = oma.."[https://omabrowser.org/oma/vps/"..ensembl.." "..gene_symbol.." - orthologs]" |
Line 528
− | :wikitext(genecards) | + | :wikitext(genecards)
:wikitext(oma) |
Tarsmf (talk) 09:39, 22 May 2024 (UTC)