Module talk:Infobox gene/Archive 2

Archive 1

Archive 2

Rendering of bgee_default is broken at SPI1

The rendering of bgee_default is broken at SPI1. Something in the logic is creating a URL link that attempts to wrap around a five-element bulleted list. This problem is also observable at Allograft inflammatory factor 1. – Jonesey95 (talk) 17:42, 11 February 2022 (UTC)

This appears to be due to an edit I did for Tarsmf, alias BgeeDB, back in October. Looking at the code, I don't know enough Lua to figure out how to unwrap the Bgee link from around the bulleted list. Hopeful that Tarsmf will be able to fix this. P.I. Ellsworth - ed. ^put'r there 14:22, 12 February 2022 (UTC)

To editor Jonesey95: in addition, there are two Linter errors, apparently identical and caused by Ibox gene, on the two pages you mention above. P.I. Ellsworth - ed. ^put'r there 16:36, 12 February 2022 (UTC)

Yes, that is why I reported the bug. – Jonesey95 (talk) 19:53, 12 February 2022 (UTC)

Okay, the October edits that added Bgee have been removed until editor Tarsmf can test them further. And btw, the Linter errors have disappeared from those two articles. P.I. Ellsworth - ed. ^put'r there 22:38, 12 February 2022 (UTC)

Bgee edit request from October 2021

Template-protected edit request on 13 October 2021 Changes to include gene expression calls via "expressed in" statements from Wikidata / Bgee database The code below adds into the Wikipedia "infobox gene" the "expressed in" assertions of human genes available in Wikidata from the Bgee database (www.bgee.org) to the "RNA expression pattern" section in the infobox. These assertions per gene are at most the top 10 anatomic entities (tissues) where a gene is expressed. The code is available in the sandbox at https://en.wikipedia.org/wiki/Module:Infobox_gene/sandbox and tested in https://en.wikipedia.org/w/index.php?title=Module_talk:Infobox_gene/testcases infobox gene testcase talk. Change preview Change preview Let us take as an example the WikidataRELN gene, the code below gets "expressed in" Wikidata property values and assign them to a "Bgee DB" row in the section "RNA expression pattern" of the infobox at Reelin gene. Click on show in the "RNA expression pattern" section to see changes FROM TO RELN Available structures PDB Ortholog search: PDBe RCSB List of PDB id codes 2ddu, 2e26, 2DDU, 2E26, 3A7Q Identifiers Aliases RELN, LIS2, PRO1598, RL, reelin, ETL7 External IDs OMIM: 600514; MGI: 103022; HomoloGene: 3699; GeneCards: RELN; OMA:RELN - orthologs Gene location (Human) Chr. Chromosome 7 (human) Band 7q22.1 Start 103,471,381 bp End 103,989,658 bp Gene location (Mouse) Chr. Chromosome 5 (mouse) Band 5 A3|5 9.98 cM Start 22,089,452 bp End 22,549,700 bp RNA expression pattern Bgee Human Mouse (ortholog) Top expressed in olfactory bulb cerebellar vermis cerebellar hemisphere paraflocculus of cerebellum right hemisphere of cerebellum spinal ganglia trigeminal ganglion endothelial cell tibial nerve pons Top expressed in ciliary body cerebellar vermis lobe of cerebellum iris olfactory bulb sciatic nerve endothelial cell of lymphatic vessel superior colliculus paraventricular nucleus of hypothalamus piriform cortex More reference expression data BioGPS More reference expression data Gene ontology Molecular function metal ion binding peptidase activity hydrolase activity serine-type peptidase activity lipoprotein particle receptor binding very-low-density lipoprotein particle receptor binding Cellular component cytoplasm dendrite plasma membrane extracellular region extracellular space membrane extracellular matrix neuron projection Biological process NMDA glutamate receptor clustering positive regulation of lateral motor column neuron migration dendrite development proteolysis cerebral cortex development lateral motor column neuron migration positive regulation of phosphatidylinositol 3-kinase signaling positive regulation of TOR signaling long-term memory multicellular organism development receptor localization to synapse postsynaptic density protein 95 clustering ventral spinal cord development protein localization to synapse forebrain development long-term potentiation regulation of gene expression layer formation in cerebral cortex cell migration learning associative learning cell adhesion hippocampus development spinal cord patterning cerebral cortex tangential migration positive regulation of peptidyl-tyrosine phosphorylation glial cell differentiation peptidyl-tyrosine phosphorylation positive regulation of excitatory postsynaptic potential positive regulation of CREB transcription factor activity positive regulation of protein kinase activity modulation of chemical synaptic transmission positive regulation of AMPA receptor activity brain development central nervous system development response to pain positive regulation of synapse maturation positive regulation of long-term synaptic potentiation cell morphogenesis involved in differentiation neuron migration positive regulation of neuron projection development positive regulation of small GTPase mediated signal transduction positive regulation of synaptic transmission, glutamatergic regulation of behavior positive regulation of dendritic spine morphogenesis reelin-mediated signaling pathway regulation of NMDA receptor activity positive regulation of protein tyrosine kinase activity axon guidance Sources:Amigo / QuickGO Orthologs Species Human Mouse Entrez 5649 19699 Ensembl ENSG00000189056 ENSMUSG00000042453 UniProt P78509 Q60841 RefSeq (mRNA) NM_173054 NM_005045 NM_011261 NM_001310464 RefSeq (protein) NP_005036 NP_774959 NP_001297393 NP_035391 Location (UCSC) Chr 7: 103.47 – 103.99 Mb Chr 5: 22.09 – 22.55 Mb PubMed search Wikidata View/Edit Human View/Edit Mouse || RELN Available structures PDB Ortholog search: PDBe RCSB List of PDB id codes 2ddu, 2e26, 2DDU, 2E26, 3A7Q Identifiers Aliases RELN, LIS2, PRO1598, RL, reelin, ETL7 External IDs OMIM: 600514; MGI: 103022; HomoloGene: 3699; GeneCards: RELN; OMA:RELN - orthologs Gene location (Human) Chr. Chromosome 7 (human) Band 7q22.1 Start 103,471,381 bp End 103,989,658 bp Gene location (Mouse) Chr. Chromosome 5 (mouse) Band 5 A3|5 9.98 cM Start 22,089,452 bp End 22,549,700 bp RNA expression pattern Bgee Human Mouse (ortholog) Top expressed in olfactory bulb cerebellar vermis cerebellar hemisphere paraflocculus of cerebellum right hemisphere of cerebellum spinal ganglia trigeminal ganglion endothelial cell tibial nerve pons Top expressed in ciliary body cerebellar vermis lobe of cerebellum iris olfactory bulb sciatic nerve endothelial cell of lymphatic vessel superior colliculus paraventricular nucleus of hypothalamus piriform cortex More reference expression data BioGPS More reference expression data Gene ontology Molecular function metal ion binding peptidase activity hydrolase activity serine-type peptidase activity lipoprotein particle receptor binding very-low-density lipoprotein particle receptor binding Cellular component cytoplasm dendrite plasma membrane extracellular region extracellular space membrane extracellular matrix neuron projection Biological process NMDA glutamate receptor clustering positive regulation of lateral motor column neuron migration dendrite development proteolysis cerebral cortex development lateral motor column neuron migration positive regulation of phosphatidylinositol 3-kinase signaling positive regulation of TOR signaling long-term memory multicellular organism development receptor localization to synapse postsynaptic density protein 95 clustering ventral spinal cord development protein localization to synapse forebrain development long-term potentiation regulation of gene expression layer formation in cerebral cortex cell migration learning associative learning cell adhesion hippocampus development spinal cord patterning cerebral cortex tangential migration positive regulation of peptidyl-tyrosine phosphorylation glial cell differentiation peptidyl-tyrosine phosphorylation positive regulation of excitatory postsynaptic potential positive regulation of CREB transcription factor activity positive regulation of protein kinase activity modulation of chemical synaptic transmission positive regulation of AMPA receptor activity brain development central nervous system development response to pain positive regulation of synapse maturation positive regulation of long-term synaptic potentiation cell morphogenesis involved in differentiation neuron migration positive regulation of neuron projection development positive regulation of small GTPase mediated signal transduction positive regulation of synaptic transmission, glutamatergic regulation of behavior positive regulation of dendritic spine morphogenesis reelin-mediated signaling pathway regulation of NMDA receptor activity positive regulation of protein tyrosine kinase activity axon guidance Sources:Amigo / QuickGO Orthologs Species Human Mouse Entrez 5649 19699 Ensembl ENSG00000189056 ENSMUSG00000042453 UniProt P78509 Q60841 RefSeq (mRNA) NM_173054 NM_005045 NM_011261 NM_001310464 RefSeq (protein) NP_005036 NP_774959 NP_001297393 NP_035391 Location (UCSC) Chr 7: 103.47 – 103.99 Mb Chr 5: 22.09 – 22.55 Mb PubMed search Wikidata View/Edit Human View/Edit Mouse Change: add line into "if" clause around line 148 Add the code below at line 148, for example. local expressed_in_tissues = check_values(p.getValue, {entity, "P5572", localNotApplicableStr, localSeparatorStr}) --P5572: expressed in Change: add "sep" as an argument of getValue function It also set sep = " " as default by replacing line 2149 CHANGE line 2145 p.getValue = function(entity, propertyID, return_val) TO p.getValue = function(entity, propertyID, return_val, sep) CHANGE line 2149 local sep = " " --could ad as input parameter if need be TO if sep == nil then sep = " " end Change: lines 212-214, to include Bgee DB conditions and arguments CHANGE if expression_images ~= "" then p.renderRNAexpression(expression_images, entrez_gene) end TO if expression_images ~= "" or expressed_in_tissues ~= localNotApplicableStr then p.renderRNAexpression(expression_images, entrez_gene, ensembl, p.renderBgeeExpression(expressed_in_tissues)) end Change: add new function to render Bgee DB "expressed in" data from Wikidata --Get the render elements title, collapse option, collapsed anatomic entities, --and anatomic entity list for the Bgee gene expression rendering. p.renderBgeeExpression = function(expressed_in_tissues) --create list of expressed in anatomic entities local bgee_title = "Bgee" bgee_title = "[https://bgee.org/ " .. bgee_title .. "]" local bgee_links = localNotApplicableStr local bgee_collapse = "none" local bgee_default = "Top expressed in" local split_bgee = mw.text.split(expressed_in_tissues, localSeparatorStr) local bgee_link_list = {} local results for k,v in ipairs(split_bgee) do if string.match(v, '%w+') and v ~= localNotApplicableStr then bgee_link_list[#bgee_link_list+1] = "\n* "..v end end --if less than 11 don't create collapsible list if table.getn(bgee_link_list) < 11 then if bgee_default == nil and table.getn(bgee_link_list) == 0 then bgee_links = localNotApplicableStr end else bgee_collapse = "collapsible collapsed" bgee_default = bgee_default .. '<br>' .. table.remove(bgee_link_list, 1) .. '<br>' .. table.remove(bgee_link_list, 1) .. '<br>' ..table.remove(bgee_link_list, 1) .. '<br>' .. table.remove(bgee_link_list, 1) .. '<br>' .. table.remove(bgee_link_list, 1) .. '<br>'--get first 5 elements in table and use for display end if bgee_link_list[#bgee_link_list] then bgee_links = table.concat(bgee_link_list, "<br>") end results = {bgee_title, bgee_collapse, bgee_default, bgee_links} return results end Change: add Bgee database to the RNA expression render function This function should replace the current one starting at line 1104. CHANGE p.renderRNAexpression = function(expression_images, entrez_gene) local title = "[[Gene expression|RNA expression]] pattern" --**lclz** local biogps_link = "[http://biogps.org/gene/"..entrez_gene.."/ More reference expression data]" --**lclz** root :tag('tr') :tag('td') :attr('colspan', 4) :css('text-align', 'center') :css('background-color', rowBGcolor) :tag('table') :attr('class', 'collapsible collapsed') :css('padding', '0') :css('border', 'none') :css('margin', '0') :css('width', '100%') :css('text-align', 'left') :tag('tr') :tag('th') :attr('colspan', '4') :css('text-align', 'center') :css('background-color', titleBGcolor) :wikitext(title) :done() --end th :done() --end tr :tag('tr') :tag('td') :attr('colspan', '4') :css('text-align', 'center') :css('background-color', rowBGcolor) :wikitext(expression_images) :done() --end td :done() --end tr :tag('tr') :tag('td') :attr('colspan', '4') :css('text-align', 'center') :css('background-color', rowBGcolor) :tag('span') :attr('class', 'plainlinks') :wikitext(biogps_link) :done() --end span :done() --end td :done() --end tr :done() --end table :done() --end td :done() --end tr end TO p.renderRNAexpression = function(expression_images, entrez_gene, ensembl, bgee_expression) local title = "[[Gene expression|RNA expression]] pattern" --**lclz** local biogps_link = "" local biogps_title = "BioGPS" biogps_title = "[http://biogps.org/ " .. biogps_title .. "]" -- If no expression image exist in BioGPS, the N/A is displayed if expression_images ~= "" then biogps_link = "[http://biogps.org/gene/"..entrez_gene.."/ More reference expression data]" --**lclz** else expression_images = localNotApplicableStr end local bgee_title = bgee_expression[1] local bgee_collapse = bgee_expression[2] local bgee_default = bgee_expression[3] local bgee_links = bgee_expression[4] local bgee_more_link = "" local ensembl_id = string.gsub(ensembl, "%s", "") if bgee_links ~= localNotApplicableStr then bgee_more_link = "[https://bgee.org/?page=gene&gene_id="..ensembl_id.." More reference expression data]" --**lclz** bgee_default = "[https://bgee.org/?page=gene&gene_id="..ensembl_id.." '''"..bgee_default.."'''] " --**lclz** else bgee_default = "" end root :tag('tr') :tag('td') :attr('colspan', 4) :css('text-align', 'center') :css('background-color', rowBGcolor) :tag('table') :attr('class', 'collapsible collapsed') :css('padding', '0') :css('border', 'none') :css('margin', '0') :css('width', '100%') :css('text-align', 'left') :tag('tr') :tag('th') :attr('colspan', '4') :css('text-align', 'center') :css('background-color', titleBGcolor) :wikitext(title) :done() --end th :done() --end tr :tag('tr') :tag('th') :attr('scope', 'row') :css('background-color', sideTitleBGcolor) :wikitext(bgee_title) :done() --end th :tag('td') :tag('table') :attr('class', bgee_collapse) :css('padding', '0') :css('border', 'none') :css('margin', '0') :css('width', '100%') :css('text-align', 'left') :tag('tr') :tag('td') :attr('colspan', '1') :tag('span') :attr('class', 'plainlinks') :wikitext(bgee_default) :done() --end span :done() --end td :done() --end tr :tag('tr') :tag('td') :attr('colspan', '1') :tag('span') :attr('class', 'plainlinks') :wikitext(bgee_links) :done() --end span :done() --end td :done() --end tr :tag('tr') :tag('td') :attr('colspan', '4') :css('text-align', 'center') :css('background-color', rowBGcolor) :tag('span') :attr('class', 'plainlinks') :wikitext(bgee_more_link) :done() --end span :done() --end td :done() --end tr :done() --end table :done() --end td :done() --end tr :tag('tr') :tag('th') :attr('scope', 'row') :css('background-color', sideTitleBGcolor) :wikitext(biogps_title) :done() --end th :tag('td') :tag('table') :attr('class', bgee_collapse) :css('padding', '0') :css('border', 'none') :css('margin', '0') :css('width', '100%') :css('text-align', 'left') :tag('tr') :tag('td') :attr('colspan', '4') :css('text-align', 'center') :css('background-color', rowBGcolor) :wikitext(expression_images) :done() --end td :done() --end tr :tag('tr') :tag('td') :attr('colspan', '4') :css('text-align', 'center') :css('background-color', rowBGcolor) :tag('span') :attr('class', 'plainlinks') :wikitext(biogps_link) :done() --end span :done() --end td :done() --end tr :done() --end table :done() --end td :done() --end tr :done() --end table :done() --end td :done() --end tr end BgeeDB (talk) 14:13, 13 October 2021 (UTC) To editor BgeeDB:  done. P.I. Ellsworth - ed. put'r there 20:22, 23 October 2021 (UTC) To editor BgeeDB:  undone. Had to revert for now; please see User talk:Paine Ellsworth#Infobox gene, which shows that this edit caused linking to disambiguation pages from mainspace articles, and that's a no-no. So this edit needs to be fixed. P.I. Ellsworth - ed. put'r there 20:56, 24 October 2021 (UTC) Reping Tarsmf since the user was renamed. * Pppery * it has begun... 21:02, 24 October 2021 (UTC) Curious, * Pppery *, if red links notify, then why wouldn't redirects notify? P.I. Ellsworth - ed. put'r there 21:07, 24 October 2021 (UTC) To editor Paine Ellsworth:Thank you all very much for noticing the ambiguity issue. To avoid any kind of ambiguity I have removed the links to Wikipedia pages. Is it okay for you? Thanks for taking care! Tarsmf (talk) 07:34, 25 October 2021 (UTC) Wish I knew more detail about LUA, but if we have your assurance that the sandbox code has been improved and will not load dab pages with a lot of article links, then yes I'm okay with it. So to be clear, you're saying that the sandbox code is ready to go? P.I. Ellsworth - ed. put'r there 09:45, 25 October 2021 (UTC) Yes, I have changed the part concerning the wikipedia links of anatomical entities to be all a simple text instead of links. You can see in the example above of the RELN gene, how it is now in the sandbox, also here https://en.wikipedia.org/w/index.php?title=Module_talk:Infobox_gene/testcases . Thanks a lot! Tarsmf (talk) 11:58, 25 October 2021 (UTC) Okay then, and  done once again. P.I. Ellsworth - ed. put'r there 12:52, 25 October 2021 (UTC) References

To make it a little easier for editor Tarsmf the October edit request has been included above in the collapsed section. P.I. Ellsworth - ed. ^put'r there 22:56, 12 February 2022 (UTC)

To editor Tarsmf: the Bgee code has been re-added to Module:Infobox gene/sandbox and the SPI1 & AIF1 infoboxes have been set up as test cases at Module talk:Infobox gene/testcases so you can see what was happening in the "RNA expression pattern" sections of the iboxes. P.I. Ellsworth - ed. ^put'r there 05:33, 14 February 2022 (UTC)

To editor Paine Ellsworth: and To editor Jonesey95: Thanks for reporting the issues. I have corrected them, please let me know if there is any other concern. The latest code is available in the sandbox at Module:Infobox gene/sandbox and tested with the reported examples at Module talk:Infobox gene/testcases. Sorry for not being able to correct it promptly, I have just seen this bug report today (I have to check why I am not receiving email notifications from Wikipedia). Tarsmf (talk) 16:48, 18 February 2022 (UTC)

To editors Tarsmf and Jonesey95: looks like this has been repaired, so the Bgee edits have been reinstated in this template. Testing should continue so that any future anomalies will be quickly fixed. P.I. Ellsworth - ed. ^put'r there 00:47, 20 February 2022 (UTC)

ensembl_id is nil

A few articles (examples: C2orf16, MKKS) are showing: "Lua error in Module:Infobox_gene at line 1153: attempt to concatenate local 'ensembl_id' (a nil value)."

That is because line 1150 is:

local ensembl_id = string.match(ensembl,"%a+%d+")

but the pattern was not found so nil was returned. Line 167 set ensembl:

local ensembl = check_values(p.getValue, {entity, "P594", localNotApplicableStr})

That's probably because MKKS (Q18032762) has no Ensembl gene ID (P594) entry. At any rate, if there is a default ensembl value that would help, it could easily be added by appending or "WHATEVER" to line 167.

By the way, the module has 18 global variables due to missing "local". I could fix them if wanted as they are undesirable. Johnuniq (talk) 02:57, 20 February 2022 (UTC)

To editors Johnuniq and Paine Ellsworth: thanks for reporting it, this issue is now corrected (latest code at Module:Infobox gene/sandbox) and tested at Module talk:Infobox gene/testcases Tarsmf (talk) 08:09, 20 February 2022 (UTC)

I changed your edit because it is much better to use Lua's conventions. Then I couldn't resist cleaning up some whitespace issues: using tabs for indents, omit trailing space. I'll leave the globals for now but they should be fixed. Johnuniq (talk) 08:49, 20 February 2022 (UTC)

thanks but now it is producing a new error for AIF1 see Module talk:Infobox gene/testcases "Lua error in Module:Infobox_gene/sandbox at line 753: attempt to perform arithmetic on local 'gend' (a string value)." Tarsmf (talk) 08:52, 20 February 2022 (UTC)

I'll have a look at that soon, I hope, but the problem has been there a while. I just edited two old revisions of Module:Infobox gene/sandbox (at 07:55, 20 February 2022 and at 16:31, 18 February 2022) and previewed them with Module talk:Infobox gene/testcases. They both show "Lua error in Module:Infobox_gene/sandbox at line 753: attempt to perform arithmetic on local 'gend' (a string value)". Johnuniq (talk) 09:06, 20 February 2022 (UTC)

Wow this is strange, because the latest version at Module talk:Infobox gene based on 16:31, 18 February 2022 does not show this error. Moreover, the variable "gend" was never edited by me Tarsmf (talk) 09:17, 20 February 2022 (UTC)

I don't follow that. Your permalink is the same as mine and I just tried it again. It gives the gend error for the testcases. Johnuniq (talk) 09:29, 20 February 2022 (UTC)

Sorry, what I was trying to say is that the deployed version for the Module:Infobox_gene 00:41, 20 February 2022 seems to be based on 16:31, 18 February 2022 and it is not showing the "gend" error for the Wikipedia gene page AIF1. Tarsmf (talk) 09:42, 20 February 2022 (UTC)

The reason gend is giving an error is that its value is a non-numeric string, namely "VALUE_ERROR (too many expensive function calls)". There might be some inefficiency in the module, or more likely, there are too many calls on the testcases page and it is blowing up. I noticed check_values and wondered if it mightn't be better to raise an error to make it clear there is a problem. Regarding gstart and gend, what should happen is that they get converted to numbers with an error displayed if that fails. Currently the code relies on Lua's quirk of silently converting numeric strings to numbers when asked to do arithmetic. That's fine, but it leads to weird error messages like this one. Johnuniq (talk) 09:47, 20 February 2022 (UTC)

The sandbox works better at the two articles cited, C2orf16 & MKKS. Question is, what might be broken elsewhere? Sandbox seems to be okay at the AIF1 article as well, which is curious as to why it gives the Lua error on the test cases page, but not in the article? P.I. Ellsworth - ed. ^put'r there 09:55, 20 February 2022 (UTC)

As figured out by Johnuniq, the arithmetic issue happens because of too many calls in the test cases page, therefore this issue will not happen in the wikipedia articles (just one call). Then, in my opinion, we can deploy the latest version edited by Johnuniq at Module:Infobox gene/sandbox, mainly to solve the issue "ensembl_id is nil". Thanks! Tarsmf (talk) 10:29, 20 February 2022 (UTC)

Then let's give it a good shot. Looks so much better at C2orf16 & MKKS! noties to Johnuniq & Tarsmf. The AIF1 test case has been split off to Module talk:Infobox gene/testcases 2. P.I. Ellsworth - ed. ^put'r there 19:32, 20 February 2022 (UTC)