Module:Infobox gene
 | This module is rated as ready for general use. It has reached a mature form and is thought to be relatively bug-free and ready for use wherever appropriate. It is ready to mention on help pages and other Wikipedia resources as an option for new users to learn. To reduce server load and bad output, it should be improved by sandbox testing rather than repeated trial-and-error editing. |
 | This module is subject to page protection. It is a highly visible module in use by a very large number of pages, or is substituted very frequently. Because vandalism or mistakes would affect many pages, and even trivial editing might cause substantial load on the servers, it is protected from editing. |
This module provides content of Template:Infobox gene.
Usage
සංස්කරණය{{#invoke:Infobox gene|getTemplateData}}{{#invoke:Infobox gene|getTemplateData|QID=Q414043}}local p = { }local navbar = require('Module:Navbar')._navbarlocal infobox = require('Module:Infobox3cols').infoboxlocal infoboxImage = require('Module:InfoboxImage').InfoboxImage-- wrapped "protected call", return "value error" with error info on errorlocal function check_values(f,args) --local u= table.upack(args)local exist, val = pcall(f, unpack(args))if exist and val ~= nil thenreturn(val)else-- Leaking some debugging info won't hurt....return("'''VALUE_ERROR''' (" .. tostring(val) .. ")")endend--texts relevant to localization are tagged with --**lclz** and/or *lclz*--on a page {{#invoke:Sandbox/genewiki/alllua|getTemplateData|QID=Q14865053}}--in debug window --frame = mw.getCurrentFrame()--frame.args = {QID="Q14865053"} Q18031325--print(p.getTemplateData(frame))p.getTemplateData = function(frame)--make some guesses about whether the provided QID is a good one--could expand here if we had some kind of error handling framework--did we get it from the pagelocal root_qid = mw.text.trim(frame.args['QID'] or "") --try to get it from the argslocal mm_qid = ""--pull all the entity objects that we will needlocalentity = {} localentity_protein = {}localentity_mouse = {}localentity_mouse_protein = {}localcheckOrtholog = "" --flag used to see if mouse data avaliablelocal mouse_propertyID = "P684" --actually ortholog property additional orthologs can existlocal protein_propertyID = "P688" --get root gene entityif root_qid == "" thenentity = mw.wikibase.getEntityObject()if entity then root_qid = entity.id else root_qid = "" endelse--assuming we think its good make one call to retrieve and store its wikidata representationentity = mw.wikibase.getEntity(root_qid)end --need to figure out if it is protein or gene herelocal subclass = p.getValue(entity, "P31") or ""if string.find(subclass, 'protein') then --if protein switch entity to geneif entity.claims then claims = entity.claims["P702"] --encoded by endif claims then--go through each index and reassign entityentity = {}if (claims[1] and claims[1].mainsnak.snaktype == "value" and claims[1].mainsnak.datavalue.type == "wikibase-entityid") thenfor k, v in pairs(claims) do --this would be problematic if multiple genes for the proteinlocal itemID = "Q" .. claims[#entity + 1].mainsnak.datavalue.value["numeric-id"]entity[#entity + 1] = mw.wikibase.getEntity(itemID)root_qid = itemIDendend --will return nothing if no claims are foundend entity = mw.wikibase.getEntity(root_qid) end--get the other related entitiesif entity thenlocal claims = "" --get protein entity object if entity.claims then claims = entity.claims[protein_propertyID] endif claims then--go through each index and then make entity_protein indexedif (claims[1] and claims[1].mainsnak.snaktype == "value" and claims[1].mainsnak.datavalue.type == "wikibase-entityid") thenfor k, v in pairs(claims) dolocal protein_itemID = "Q" .. claims[#entity_protein + 1].mainsnak.datavalue.value["numeric-id"]entity_protein[#entity_protein + 1] = mw.wikibase.getEntity(protein_itemID)endend --will return nothing if no claims are foundend --get mouse entity object if entity.claims thenclaims = entity.claims[mouse_propertyID]endlocal qualifierID = "P703" --found in taxonlocal mouse_qual = "Q83310"if claims thenif (claims[1] and claims[1].mainsnak.snaktype == "value" and claims[1].mainsnak.datavalue.type == "wikibase-entityid") thenfor k, v in pairs(claims) doif checkOrtholog == 1 then -- Don't have to go on if we already got itbreakend local mouse_itemID = "Q" .. v.mainsnak.datavalue.value["numeric-id"]local quals if v.qualifiers thenquals = v.qualifiers.P703endif quals thenfor qk, qv in pairs(quals) do--get the taxon qualifier idlocal qual_obj_id = "Q"..qv.datavalue.value["numeric-id"]if qual_obj_id == mouse_qual then --check if this is mouse or othermm_qid = mouse_itemID entity_mouse = mw.wikibase.getEntity(mouse_itemID)checkOrtholog = 1breakendendendendend --will return nothing if no claims are foundelsecheckOrtholog = 0end --get mouse protein entity object if entity_mouse and entity_mouse.claims thenclaims = entity_mouse.claims[protein_propertyID]end if claims then if (claims[1] and claims[1].mainsnak.snaktype == "value" and claims[1].mainsnak.datavalue.type == "wikibase-entityid") thenfor k, v in pairs(claims) dolocal protein_itemID = "Q" .. claims[#entity_mouse_protein + 1].mainsnak.datavalue.value["numeric-id"]entity_mouse_protein[#entity_mouse_protein + 1] = mw.wikibase.getEntity(protein_itemID)endend --will return nothing if no claims are found endendif entity then --only require the main gene entity--a list variables of all the data in the info boxlocal name = check_values(p.getLabel,{entity})local entrez_gene = check_values(p.getValue, {entity, "P351", "n/a"} )local entrez_gene_mm = check_values(p.getValue, {entity_mouse, "P351", "n/a"})local image = check_values( p.getImage, {entity, "P18", " ", "250px"}) --need to set sizelocal uniprotID_hs = check_values(p.getValueProtein, {entity_protein, "P352", "n/a"}) local uniprotID_mm = check_values(p.getValueProtein, {entity_mouse_protein, "P352", "n/a"}) local pdbIDs = check_values(p.getPDB, {entity_protein}) --makes a list with links to RCSB local aliases = check_values(p.getAliases, {entity}) local gene_symbol = check_values(p.getValue, {entity, "P353"}) local hgnc_id = check_values(p.getValue, {entity, "P354"}) local homologene_id = check_values(p.getValue, {entity, "P593"}) local omim_id = check_values(p.getValue, {entity, "P492"}) local mgi_id = check_values(p.getValue, {entity_mouse, "P671"}) local ChEMBL_id = check_values(p.getValue, {entity_protein, "P592"}) local IUPHAR_id = check_values(p.getValue, {entity_protein, "P595"}) local ec_no = check_values(p.getValueProtein, {entity_protein, "P591"}) local mol_funct = check_values(p.getGO, {entity_protein, "P680"}) local cell_comp = check_values(p.getGO, {entity_protein, "P681"}) local bio_process = check_values(p.getGO, {entity_protein, "P682"}) local expression_images = check_values(p.getImage, {entity,"P692","<br><br>","250px"}) local ensembl = check_values(p.getValue, {entity, "P594", "n/a"}) local ensembl_mm = check_values(p.getValue, {entity_mouse, "P594", "n/a"}) local refseq_mRNA = check_values(p.getRefseq_mRNA, {entity, "P639", "n/a"}) local refseq_mRNA_mm = check_values(p.getRefseq_mRNA, {entity_mouse, "P639", "n/a"}) local refseq_prot = check_values(p.getRefseq_protein, {entity_protein, "P637", "n/a"}) local refseq_prot_mm = check_values(p.getRefseq_protein, {entity_mouse_protein, "P637", "n/a"})local gstart = check_values(p.getChromosomeLoc, {entity, "P644", "hg"})local gend = check_values(p.getChromosomeLoc, {entity, "P645", "hg"})local chr = check_values(p.trimChromosome, {entity}) local cytoband = check_values(p.getValue, {entity, "P4196", "n/a"})local db = check_values(p.getAliasFromGenomeAssembly, {entity,"hg"}) local gstart_mm = check_values(p.getChromosomeLoc, {entity_mouse, "P644", "mm"})local gend_mm = check_values(p.getChromosomeLoc, {entity_mouse, "P645", "mm"})local chr_mm = check_values( p.trimChromosome, {entity_mouse})local db_mm = check_values(p.getAliasFromGenomeAssembly, {entity_mouse,"mm"}) local cytoband_mm = check_values(p.getValue, {entity_mouse, "P4196", "n/a"})local disease, dis_ref = ''if p.getDisease(entity, "P2293") then disease, dis_ref = p.getDisease(entity, "P2293") else disease, dis_ref = {"'''VALUE_ERROR'''","'''VALUE_ERROR'''" } endif p.getDrug(entity_protein, "P129") then drug, drug_ref, drug_pqid, drug_pname = p.getDrug(entity_protein, "P129") else drug, drug_ref, drug_pqid, drug_pname = {"'''VALUE_ERROR'''","'''VALUE_ERROR'''" } end--local drug = check_values(p.getDrug, {entity_protein, "P129"})--define Global Color SchemerowBGcolor = '#eee'titleBGcolor = '#ddd'sideTitleBGcolor = '#c3fdb8'p.createTable() p.renderUpperTitle(name) --p.renderCaption() p.renderImage(image) p.renderAvailableStructures(uniprotID_hs, uniprotID_mm, checkOrtholog, pdbIDs) --PDB infop.renderIdentifiers(aliases, hgnc_id, gene_symbol, homologene_id, omim_id, mgi_id, ChEMBL_id, IUPHAR_id, ec_no, entrez_gene)--uncomment here to add a section of the infobox about genetically related diseases, with references--if (disease ~= "" and dis_ref ~= "") then --removes section from those items without disease info--p.renderDiseases(frame, disease, dis_ref, name, root_qid)--end --uncomment here to add a section of the infobox about drugs that target the protein product of this gene, with references--if (drug ~= "" ) then --removes section from those items without drug info--p.renderDrug(frame,drug, drug_ref, drug_pqid, drug_pname) --endif (chr ~= "" and gstart ~= "" and gend ~= "") or (chr_mm ~= "" and gstart_mm ~= "" and gend_mm ~= "") thenp.renderGeneLocation(frame, chr, gstart, gend, db, cytoband, ensembl, chr_mm, gstart_mm, gend_mm, db_mm, cytoband_mm, ensembl_mm, name)endif expression_images ~= "" thenp.renderRNAexpression(expression_images, entrez_gene)endif (mol_funct ~= "" and cell_comp ~= "" and bio_process ~= "") thenp.renderGeneOntology(mol_funct, cell_comp, bio_process, uniprotID_hs)endp.renderOrthologs(frame, entrez_gene, entrez_gene_mm, ensembl, ensembl_mm, uniprotID_hs, uniprotID_mm, refseq_mRNA, refseq_mRNA_mm, refseq_prot, refseq_prot_mm, db, chr, gstart, gend, db_mm, chr_mm, gstart_mm, gend_mm)p.renderFooter(root_qid, mm_qid) return tostring(root) --return table.concat(drug_pqid) else return "An Error has occurred retrieving Wikidata item for infobox"endendp.createTable = function(subbox) if subbox == 'sub' then --doesn't work root :tag('table') :css('padding', '0') :css('border', 'none') :css('margin', '0') :css('width', 'auto') :css('min-width', '100%') :css('font-size', '100%') :css('clear', 'none') :css('float', 'none') :css('background-color', 'transparent') else root = mw.html.create('table') root -- *lclz*: Some projects, like zhwiki (again), use inline styles on -- infobox modules in addition to the class. Be sure to check them out. :addClass('infobox') :css('width', '26.4em') endend--Title above imagep.renderUpperTitle = function(name)local title = name if not title then return "error: failed to get label"; end root :tag('tr') :tag('th') :attr('colspan', 4) :css('text-align', 'center') :css('font-size', '125%') :css('font-weight', 'bold') :wikitext(title) :done() --end th :done() --end trend--This is a place holder for the image caption, which is stored in wikicommons comments unsure how to access p.renderCaption = function(entity)--captionend--gets default imagep.renderImage = function(image)root:tag('tr') :tag('td') :attr('colspan', 4) :css('text-align', 'center') :wikitext(image) :done() --end td :done() --end tr endp.renderAvailableStructures = function(uniprotID_hs, uniprotID_mm, checkOrtholog, pdbIDs) local title = 'Available structures' --**lclz** local pdb_link = "[[Protein_Data_Bank|PDB]]" --**lclz** local searchTitle = "" local listTitle = "List of PDB id codes" --**lclz** local PDBe_base = 'https://www.ebi.ac.uk/pdbe/searchResults.html?display=both&term=' local RCSB_base = 'http://www.rcsb.org/pdb/search/smartSubquery.do?smartSearchSubtype=UpAccessionIdQuery&accessionIdList=' local url_uniprot = " " if checkOrtholog == 1 and uniprotID_mm ~= 'n/a' then searchTitle = 'Ortholog search: ' url_uniprot = uniprotID_mm..','..uniprotID_hs else searchTitle = 'Human UniProt search: ' url_uniprot = uniprotID_hs end local PDBe_list = " " --create a list with " or " if there is more than one uniprot --get first uniprot in a listif url_uniprot:match("([^,]+),") then--first check if there is a list if not just assume one valuePDBe_list = string.gsub(url_uniprot, ",", "%%20or%%20") --add or's inststead of commaselsePDBe_list = url_uniprotend local PDBe = "["..PDBe_base..PDBe_list.." PDBe] " local RCSB = "["..RCSB_base..url_uniprot.." RCSB] " if string.match(pdbIDs, '%w+') then --if there aren't any PDB_ID don't display this part of the infobox --p.formatRow(title)---how to not close the tags is a mystery and I could condense code once I figure out root :tag('tr') :tag('td') :attr('colspan', 4) :css('text-align', 'center') :css('background-color', rowBGcolor) :tag('table') :css('padding', '0') :css('border', 'none') :css('margin', '0') :css('width', '100%') :css('text-align', 'left') :tag('tr') --create title header :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('rowspan', '2') :css('background-color', sideTitleBGcolor) :css('width', '43px') :wikitext(pdb_link) :done() --end th :tag('td') :attr('colspan', '2') :css('background-color', rowBGcolor) :wikitext(searchTitle) :tag('span') :attr('class', 'plainlinks') :wikitext(PDBe) :wikitext(RCSB) :done() --end span :done() --end td :done() --end tr :tag('tr') --new row for collapsible list of PDB codes :tag('td') :tag('table') :attr('class', 'collapsible collapsed') :css('padding', '0') :css('border', 'none') :css('margin', '0') :css('width', '100%') :css('text-align', 'left') :tag('tr') :css('background-color',titleBGcolor) :css('text-align', 'center') :tag('th') :attr('colspan', '2') :wikitext(listTitle) :done() --end th :done() --end tr :tag('tr') :tag('td') :attr('colspan', '2') :css('background-color', rowBGcolor) :tag('p') :tag('span') :attr('class', 'plainlinks') :wikitext(pdbIDs) :done() --end span :done() --end p :done() --end td :done() --end tr :done() --end table :done() --end td :done() --end tr :done() --end table :done() --end td :done() --end tr else return ""endendp.renderIdentifiers = function(aliases, hgnc_id, gene_symbol, homologene_id, omim_id, mgi_id, ChEMBL_id, IUPHAR_id, ec_no, entrez_gene)local title = "Identifiers" --**lclz**local label_aliases = "[[Gene nomenclature|Aliases]]" --**lclz**local symbol_url if gene_symbol == "" or gene_symbol == nil thensymbol_url = ""elseif hgnc_id == "" or hgnc_id == nil thensymbol_url = gene_symbolelsesymbol_url = "[https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/"..hgnc_id.." "..gene_symbol.."]"end end-- *lclz*: see getAliases. You can, say, use another punctuation for your language. aliases = string.gsub(aliases, ', '..gene_symbol..'$', '') --get rid of gene name if last in alias list aliases = string.gsub(aliases, gene_symbol..', ', '') --get rid of gene name if first in aliases list aliases = string.gsub(aliases, ', '..gene_symbol..',', ',') --get rid of gene name if in aliases list aliases = string.gsub(aliases, ", ,", ",") --remove comma from middle aliases = string.gsub(aliases, ", $", "") --remove comma from endlocal label_ext_id = "External IDs" --**lclz**omim_id = string.gsub(omim_id, "%s", "")local omim_list = mw.text.split(omim_id, ",")local omim = ""if (omim_id ~= nil and omim_id ~= "") thenomim = "[[Mendelian_Inheritance_in_Man|OMIM:]]".." " --**lclz**endfor i, v in ipairs(omim_list) doif string.match(v, '%w+') thenomim = omim.."[https://omim.org/entry/"..v.." "..v.."], "endendomim = string.gsub(omim, ", $"," ")--remove comma from endhomologene_id = string.gsub(homologene_id, "%s", "")local homolo_list = mw.text.split(homologene_id, ",")local homolo =""if (homologene_id ~= nil and homologene_id ~= "") thenhomolo = "[[HomoloGene|HomoloGene:]]".." "endfor i, v in ipairs(homolo_list) doif string.match(v, '%w+') thenhomolo = homolo.."[https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=homologene&dopt=HomoloGene&list_uids="..v.." "..v.."] "endendhomolo = string.gsub(homolo, ", $"," ")--remove comma from endlocal genecards = "[[GeneCards|GeneCards:]]".." "genecards = genecards.."[https://www.genecards.org/cgi-bin/carddisp.pl?gene="..gene_symbol.." "..gene_symbol.."] "mgi_id = string.gsub(mgi_id, "%s", "")local mgi_list = mw.text.split(mgi_id, ",")local mgi = "" if (mgi_id ~= nil and mgi_id ~= "") thenmgi = "[[Mouse_Genome_Informatics|MGI:]]".." " --**lclz**endfor i, v in ipairs(mgi_list) doif string.match(v, '%w+') thenlocal mgi_number = string.sub(mgi_id, 5)mgi = mgi.."[http://www.informatics.jax.org/marker/"..mgi_id.." "..mgi_number.."] "endendmgi = string.gsub(mgi, ", $"," ")--remove comma from endlocal ChEMBL = ""if string.match(ChEMBL_id, '%w+') thenChEMBL = "[[ChEMBL|ChEMBL:]]".." ".."[https://www.ebi.ac.uk/chembldb/index.php/target/inspect/CHEMBL"..ChEMBL_id.." "..ChEMBL_id.."] "endlocal IUPHAR = ""if string.match(IUPHAR_id, '%w+') then IUPHAR = "[[International_Union_of_Basic_and_Clinical_Pharmacology|IUPHAR:]]".." ".."[http://www.guidetopharmacology.org/GRAC/ObjectDisplayForward?objectId="..IUPHAR_id.." "..IUPHAR_id.."] " --**lclz**end -- *lclz*local label_EC = "[[Enzyme_Commission_number|EC number]]" --**lclz**ec_no = string.gsub(ec_no, "%d%.%d+%.%d+%.%-,", "")--remove those with"-" in listec_no = string.gsub(ec_no, "%d%.%d+%.%d+%.%-", "")--remove those with"-" not in listlocal link_ec_no = string.gsub(ec_no, "," ,"+") --create format for linklocal EC = "[https://www.genome.jp/dbget-bin/www_bget?enzyme+" .. link_ec_no .. " " .. ec_no .. "]"root: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) :tag('span') :attr('class', 'plainlinks') :wikitext(label_aliases) :done() --end span :done() --end th :tag('td') :attr('colspan','3') :css('background', rowBGcolor) :tag('span') :attr('class', 'plainlinks') :wikitext(symbol_url) :done() --end span :wikitext(aliases) :done() --end td :done() --end tr :done() --end tr :tag('tr') :tag('th') :attr('scope', 'row') :css('background-color', sideTitleBGcolor) :wikitext(label_ext_id) :done() --end th :tag('td') :attr('colspan', '3') :css('background-color', rowBGcolor) :tag('span') :attr('class', 'plainlinks') :wikitext(omim) :wikitext(mgi) :wikitext(homolo) :wikitext(ChEMBL) :wikitext(IUPHAR) :wikitext(genecards) :done() --end span :done() --end td :done() --end trif ec_no ~= "" then root :tag('tr') :tag('th') :attr('scope', 'row') :css('background-color', sideTitleBGcolor) :wikitext(label_EC) :done() --end th :tag('td') :attr('colspan', '3') :css('background-color', rowBGcolor) :tag('span') :attr('class', 'plainlinks') :wikitext(EC) :done() --end span:done() --end td:done() --end tr endendp.renderDiseases = function(frame, disease, dis_ref, name, qid) local title = "Genetically Related Diseases" --**lclz**--check first to see if any of the diseases have referenceslocal ref_flag_all = false --check if any disease have references if not then don't render the headerslocal disease_name = '' --local disease_name = table.concat(disease, ", ")for index,value in ipairs(disease) doif (dis_ref[index] ~= nil and dis_ref[index] ~= '') thenif disease_name == '' thendisease_name = valueelsedisease_name = disease_name..", "..value -- *lclz*: punctuationendref_flag_all = trueendend if ref_flag_all then root:tag('tr'):tag('td') :attr('colspan', 4) :css('text-align', 'center') :css('background-color', rowBGcolor):tag('tr') --create title bar:tag('th'):attr('colspan', '3'):css('text-align', 'center'):css('background-color', titleBGcolor):wikitext(title):done() --end th:done() --end tr:done() --end td:done() --end tr local ref_url = "https://www.wikidata.org/wiki/"..qid.."#P2293" --direct page to property genetically associated diseaselocal title = "Diseases that are genetically associated with "..name.." view/edit references on wikidata"local ref_link = disease_name..frame:extensionTag("ref",frame:expandTemplate{ title = 'cite_web', args = { title = title, url = ref_url} })root:tag('tr') :attr('colspan', 4) :css('text-align', 'center') :css('background-color', rowBGcolor):tag('td'):css('background-color', rowBGcolor):attr('scope', 'row'):attr('colspan', '3'):wikitext(ref_link):done() --end td :done() --end tr end end p.renderDrug = function(frame,drug, drug_ref, drug_pqid, drug_pname) local title = "Targeted by Drug" --**lclz** --check first to see if any of the drugs have referenceslocal ref_flag_all = false --check if any drugs have references if not then don't render the headersdrug_list_per_protein = {} -- a list of lists of drugs to put in reference string each protein will have a list --for i,v in ipairs(drug_pqid) do -- set all lists keys to empty so can append without key errors --endfor index,value in ipairs(drug) doif (drug_ref[index] ~= nil and drug_ref[index] ~= '') thenprotein_qid = drug_pqid[index]if drug_list_per_protein[protein_qid] == '' or drug_list_per_protein[protein_qid] == nil thendrug_list_per_protein[protein_qid] = valueelse-- *lclz*: comma drug_list_per_protein[protein_qid] = drug_list_per_protein[protein_qid]..', '..value --each list of drugs keyed on protein qid endref_flag_all = trueendend if ref_flag_all then root:tag('tr'):tag('td') :attr('colspan', 4) :css('text-align', 'center') :css('background-color', rowBGcolor):tag('tr') --create title bar:tag('th'):attr('colspan', '3'):css('text-align', 'center'):css('background-color', titleBGcolor):wikitext(title):done() --end th:done() --end tr:done() --end td:done() --end tr --loop to create reference links from drug lists for k,v in pairs(drug_list_per_protein) do local drug_name = v local ref_url = "https://www.wikidata.org/wiki/"..k.."#P129" --direct page to property genetically associated disease local title = "Drugs that physically interact with "..drug_pname[k].." view/edit references on wikidata" local ref_link = drug_name..frame:extensionTag("ref",frame:expandTemplate{ title = 'cite_web', args = { title = title, url = ref_url} }) root :tag('tr') :attr('colspan', 4) :css('text-align', 'center') :css('background-color', rowBGcolor):tag('td'):css('background-color', rowBGcolor):attr('scope', 'row'):attr('colspan', '3'):wikitext(ref_link):done() --end td :done() --end tr end end endp.renderGeneLocation = function(frame, chr, gstart, gend, db, cytoband, ensembl, chr_mm, gstart_mm, gend_mm, db_mm, cytoband_mm, ensembl_mm, name)local titleHuman = "Gene location (Human)" --**lclz**local titleMouse = "Gene location (Mouse)" --**lclz** local label_chr = "[[Chromosome|Chr.]]" --**lclz** local label_locus = "[[Locus (genetics)|Band]]" --**lclz** local label_gstart = "Start" --**lclz** local label_gend = "End" --**lclz**local tooltip_arrowSign = "Genomic location for "..name --**lclz** local arrowSign_width = 14if chr ~= "" and gstart ~= "" and gend ~= "" then--Chromosome lengths are from GRCh38.p10 https://www.ncbi.nlm.nih.gov/grc/human/data?asm=GRCh38.p10--This table is used only for calculating "Where should red-rectangle put?"--Curretly, Aug 2017, it seems all gene data, which are stored in Wikidata, have start/end positions based on GRCh38.local chrLengthTable = {}chrLengthTable["1"] = 248956422chrLengthTable["2"] = 242193529 chrLengthTable["3"] = 198295559 chrLengthTable["4"] = 190214555 chrLengthTable["5"] = 181538259 chrLengthTable["6"] = 170805979 chrLengthTable["7"] = 159345973 chrLengthTable["8"] = 145138636 chrLengthTable["9"] = 138394717 chrLengthTable["10"] = 133797422 chrLengthTable["11"] = 135086622 chrLengthTable["12"] = 133275309 chrLengthTable["13"] = 114364328 chrLengthTable["14"] = 107043718 chrLengthTable["15"] = 101991189 chrLengthTable["16"] = 90338345 chrLengthTable["17"] = 83257441 chrLengthTable["18"] = 80373285 chrLengthTable["19"] = 58617616 chrLengthTable["20"] = 64444167 chrLengthTable["21"] = 46709983 chrLengthTable["22"] = 50818468 chrLengthTable["X"] = 156040895 chrLengthTable["Y"] = 57227415chrLengthTable["MT"] = 16569local chrLength = chrLengthTable[chr]--Different languages have different word order.local chrTextTable = {}--**lclz**chrTextTable["1"] = "Chromosome 1 (human)"chrTextTable["2"] = "Chromosome 2 (human)"chrTextTable["3"] = "Chromosome 3 (human)"chrTextTable["4"] = "Chromosome 4 (human)"chrTextTable["5"] = "Chromosome 5 (human)"chrTextTable["6"] = "Chromosome 6 (human)"chrTextTable["7"] = "Chromosome 7 (human)"chrTextTable["8"] = "Chromosome 8 (human)"chrTextTable["9"] = "Chromosome 9 (human)"chrTextTable["10"] = "Chromosome 10 (human)"chrTextTable["11"] = "Chromosome 11 (human)"chrTextTable["12"] = "Chromosome 12 (human)"chrTextTable["13"] = "Chromosome 13 (human)"chrTextTable["14"] = "Chromosome 14 (human)"chrTextTable["15"] = "Chromosome 15 (human)"chrTextTable["16"] = "Chromosome 16 (human)"chrTextTable["17"] = "Chromosome 17 (human)"chrTextTable["18"] = "Chromosome 18 (human)"chrTextTable["19"] = "Chromosome 19 (human)" chrTextTable["20"] = "Chromosome 20 (human)"chrTextTable["21"] = "Chromosome 21 (human)"chrTextTable["22"] = "Chromosome 22 (human)"chrTextTable["X"] = "X chromosome (human)"chrTextTable["Y"] = "Y chromosome (human)"chrTextTable["MT"] = "Mitochondrial DNA (human)"local chrText = chrTextTable[chr]--about the calculation below, see https://www.how.com.vn/wiki/en/User:Was_a_bee/Gene#3._Calculation_detaillocal markerWidth = ((gend - gstart) * 294.133 )/ chrLengthif markerWidth < 2 thenmarkerWidth = 2elsemarkerWidth = math.ceil(markerWidth)endlocal markerLocation = (147.0666 * (gstart + gend) / chrLength ) + 1.6 - (markerWidth / 2)local arrowSignLocation = markerLocation + (markerWidth / 2) - (arrowSign_width / 2)markerLocation = math.floor( markerLocation * 10 + 0.5 ) / 10local source_link_chr = ""local source_link_gstart = ""local source_link_gend = ""if( db == "hg38" ) thensource_link_chr = frame:extensionTag("ref", "[http://May2017.archive.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g="..ensembl.." GRCh38: Ensembl release 89: "..ensembl.."] - [[Ensembl genome database project|Ensembl]], May 2017", {name = "refGRCh38Ensembl"}) --**lclz**source_link_gstart = frame:extensionTag("ref", "", {name = "refGRCh38Ensembl"})source_link_gend = frame:extensionTag("ref", "", {name = "refGRCh38Ensembl"})elseif( db == "hg37") thensource_link_chr = frame:extensionTag("ref", "[http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;&g="..ensembl.." GRCh37: Ensembl release 89: "..ensembl.."] - [[Ensembl genome database project|Ensembl]], May 2017", {name = "refGRCh37Ensembl"}) --**lclz**source_link_gstart = frame:extensionTag("ref", "", {name = "refGRCh37Ensembl"})source_link_gend = frame:extensionTag("ref", "", {name = "refGRCh37Ensembl"})elsesource_link = ""source_link_gstart = ""source_link_gend = ""endlocal wikitext_for_ideogram_image = "" --wikitext used for showing gene locationif chr == "MT" then -- wikitext for mitochondrial DNA--wikitext_for_ideogram_image = wikitext_for_ideogram_image.."<div align=\"center\">"--wikitext_for_ideogram_image = wikitext_for_ideogram_image.."<div style=\"position\: relative\; width\: 300px\;\">"--wikitext_for_ideogram_image = wikitext_for_ideogram_image.."[[File:Map of the human mitochondrial genome.svg|300px|"..chrText.."]]"--wikitext_for_ideogram_image = wikitext_for_ideogram_image.."</div>"--wikitext_for_ideogram_image = wikitext_for_ideogram_image.."</div>"else -- wikitext for autosome and sex chromosomewikitext_for_ideogram_image = wikitext_for_ideogram_image.."<div align=\"center\">"wikitext_for_ideogram_image = wikitext_for_ideogram_image.."<div style=\"position\: relative\; width\: 300px\;\">"wikitext_for_ideogram_image = wikitext_for_ideogram_image.."[[File:Human chromosome "..chr.." ideogram.svg|300px|"..chrText.."]]"wikitext_for_ideogram_image = wikitext_for_ideogram_image.."<div style=\"position\: absolute\; left\: "..arrowSignLocation.."px\; top\: 2px\; padding\: 0\;\">"wikitext_for_ideogram_image = wikitext_for_ideogram_image.."[[File:HSR 1996 II 3.5e.svg|"..arrowSign_width.."px|"..tooltip_arrowSign.."]]</div>"wikitext_for_ideogram_image = wikitext_for_ideogram_image.."<div style=\"position\: absolute\; left\: "..markerLocation.."px\; top\: 19px\; padding\: 0\;\">[[File:Red rectangle "..markerWidth.."x18.png|"..markerWidth.."px|"..tooltip_arrowSign.."]]</div>"wikitext_for_ideogram_image = wikitext_for_ideogram_image.."</div>"wikitext_for_ideogram_image = wikitext_for_ideogram_image.."</div>"endroot:tag('tr') :tag('td') :attr('colspan', 4) :css('text-align', 'center') :css('background-color', rowBGcolor) :tag('table') :attr('class', 'collapsible expand') :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(titleHuman):done() --end th:done() --end tr:tag('tr'):tag('td'):attr('colspan', '4'):css('text-align', 'center'):css('background-color', rowBGcolor):wikitext("[[File:Ideogram human chromosome "..chr..".svg|300px|"..chrText.."]]"):done() --end td:done() --end tr:tag('tr'):tag('th'):attr('scope', 'row'):attr('width', '15%'):css('background-color', sideTitleBGcolor):wikitext(label_chr):done() --end th:tag('td'):attr('colspan', '3'):attr('width', '85%'):css('background-color', rowBGcolor):tag('span'):attr('class', 'plainlinks'):wikitext("[["..chrText.."]]"..source_link_chr):done() --end span :done() --end td:done() --end tr:tag('tr'):tag('td'):attr('colspan', '4'):css('text-align', 'center'):css('background-color', rowBGcolor):wikitext(wikitext_for_ideogram_image):done() --end td:done() --end tr:tag('tr'):tag('th'):attr('scope', 'row'):attr('rowspan', '2'):attr('width', '15%'):css('background-color', sideTitleBGcolor):wikitext(label_locus):done() --end th:tag('td'):attr('rowspan', '2'):attr('width', '35%'):css('background-color', rowBGcolor):tag('span'):attr('class', 'plainlinks'):wikitext(cytoband):done() --end span :done() --end td:tag('th'):attr('scope', 'row'):css('background-color', sideTitleBGcolor):wikitext(label_gstart):done() --end th:tag('td'):css('background-color', rowBGcolor):tag('span'):attr('class', 'plainlinks'):wikitext(p.separateWithComma(gstart).." [[Base pair|bp]]"..source_link_gstart):done() --end span :done() --end td:done() --end tr:tag('tr'):tag('th'):attr('scope', 'row'):css('background-color', sideTitleBGcolor):wikitext(label_gend):done() --end th:tag('td'):css('background-color', rowBGcolor):tag('span'):attr('class', 'plainlinks'):wikitext(p.separateWithComma(gend).." [[Base pair|bp]]"..source_link_gend):done() --end span :done() --end td:done() --end tr:done() --end table :done() --end td:done() --end trendif chr_mm ~= "" and gstart_mm ~= "" and gend_mm ~= "" then--Chromosome lengths are from GRCm38.p5 https://www.ncbi.nlm.nih.gov/grc/mouse/data?asm=GRCm38.p5local chrLengthTable_mm = {}chrLengthTable_mm["1"] = 195471971chrLengthTable_mm["2"] = 182113224chrLengthTable_mm["3"] = 160039680chrLengthTable_mm["4"] = 156508116chrLengthTable_mm["5"] = 151834684chrLengthTable_mm["6"] = 149736546 chrLengthTable_mm["7"] = 145441459 chrLengthTable_mm["8"] = 129401213 chrLengthTable_mm["9"] = 124595110 chrLengthTable_mm["10"] = 130694993 chrLengthTable_mm["11"] = 122082543 chrLengthTable_mm["12"] = 120129022chrLengthTable_mm["13"] = 120421639 chrLengthTable_mm["14"] = 124902244chrLengthTable_mm["15"] = 104043685chrLengthTable_mm["16"] = 98207768chrLengthTable_mm["17"] = 94987271 chrLengthTable_mm["18"] = 90702639 chrLengthTable_mm["19"] = 61431566 chrLengthTable_mm["X"] = 171031299chrLengthTable_mm["Y"] = 91744698chrLengthTable_mm["MT"] = 16299local chrLength_mm = chrLengthTable_mm[chr_mm]--Different languages have different word order.local chrTextTable_mm = {}--**lclz**chrTextTable_mm["1"] = "Chromosome 1 (mouse)"chrTextTable_mm["2"] = "Chromosome 2 (mouse)"chrTextTable_mm["3"] = "Chromosome 3 (mouse)"chrTextTable_mm["4"] = "Chromosome 4 (mouse)"chrTextTable_mm["5"] = "Chromosome 5 (mouse)"chrTextTable_mm["6"] = "Chromosome 6 (mouse)"chrTextTable_mm["7"] = "Chromosome 7 (mouse)"chrTextTable_mm["8"] = "Chromosome 8 (mouse)"chrTextTable_mm["9"] = "Chromosome 9 (mouse)"chrTextTable_mm["10"] = "Chromosome 10 (mouse)"chrTextTable_mm["11"] = "Chromosome 11 (mouse)"chrTextTable_mm["12"] = "Chromosome 12 (mouse)"chrTextTable_mm["13"] = "Chromosome 13 (mouse)"chrTextTable_mm["14"] = "Chromosome 14 (mouse)"chrTextTable_mm["15"] = "Chromosome 15 (mouse)"chrTextTable_mm["16"] = "Chromosome 16 (mouse)"chrTextTable_mm["17"] = "Chromosome 17 (mouse)"chrTextTable_mm["18"] = "Chromosome 18 (mouse)"chrTextTable_mm["19"] = "Chromosome 19 (mouse)" chrTextTable_mm["X"] = "X chromosome (mouse)"chrTextTable_mm["Y"] = "Y chromosome (mouse)" chrTextTable_mm["MT"] = "Mitochondrial DNA (mouse)" local chrText_mm = chrTextTable_mm[chr_mm]--about the calculation below, see https://www.how.com.vn/wiki/en/User:Was_a_bee/Gene#3._Calculation_detaillocal markerWidth_mm = ((gend_mm - gstart_mm) * 294.133 )/ chrLength_mmif markerWidth_mm < 2 thenmarkerWidth_mm = 2elsemarkerWidth_mm = math.ceil(markerWidth_mm)endlocal markerLocation_mm = (147.0666 * (gstart_mm + gend_mm) / chrLength_mm ) + 1.6 - (markerWidth_mm / 2)local arrowSignLocation_mm = markerLocation_mm + (markerWidth_mm / 2) - (arrowSign_width / 2)markerLocation_mm = math.floor( markerLocation_mm * 10 + 0.5 ) / 10local source_link_chr_mm = ""local source_link_gstart_mm = ""local source_link_gend_mm = ""if( db_mm == "mm10" or db_mm == "mm0") then--"mm0" happens because of function "getAliasFromGenomeAssembly()" is not prepared for mouse data.--But as of now, Aug. 2017, it seems that all data which is stored in Wikidata are based on GRCm38/mm10.--So treating mouse genomic data as GRCm38/mm10 if not specified.source_link_chr_mm = frame:extensionTag("ref", "[http://May2017.archive.ensembl.org/Mus_musculus/Gene/Summary?db=core;g="..ensembl_mm.." GRCm38: Ensembl release 89: "..ensembl_mm.."] - [[Ensembl genome database project|Ensembl]], May 2017", {name = "refGRCm38Ensembl"}) --**lclz**source_link_gstart_mm = frame:extensionTag("ref", "", {name = "refGRCm38Ensembl"}) source_link_gend_mm = frame:extensionTag("ref", "", {name = "refGRCm38Ensembl"}) elsesource_link_chr_mm = ""source_link_gstart_mm = ""source_link_gend_mm = ""endlocal wikitext_for_ideogram_image_mm = "" --wikitext used for showing gene locationif chr_mm == "MT" then -- wikitext for mitochondrial DNA--wikitext_for_ideogram_image_mm = wikitext_for_ideogram_image_mm.."<div align=\"center\">"--wikitext_for_ideogram_image_mm = wikitext_for_ideogram_image_mm.."<div style=\"position\: relative\; width\: 300px\;\">"--wikitext_for_ideogram_image_mm = wikitext_for_ideogram_image_mm.."[[File:Map of the human mitochondrial genome.svg|300px|"..chrText_mm.."]]"--wikitext_for_ideogram_image_mm = wikitext_for_ideogram_image_mm.."</div>"--wikitext_for_ideogram_image_mm = wikitext_for_ideogram_image_mm.."</div>"else -- wikitext for autosome and sex chromosomewikitext_for_ideogram_image_mm = wikitext_for_ideogram_image_mm.."<div align=\"center\">"wikitext_for_ideogram_image_mm = wikitext_for_ideogram_image_mm.."<div style=\"position\: relative\; width\: 300px\;\">"wikitext_for_ideogram_image_mm = wikitext_for_ideogram_image_mm.."[[File:Ideogram of house mouse chromosome "..chr_mm..".svg|300px|"..chrText_mm.."]]"wikitext_for_ideogram_image_mm = wikitext_for_ideogram_image_mm.."<div style=\"position\: absolute\; left\: "..arrowSignLocation_mm.."px\; top\: 2px\; padding\: 0\;\">"wikitext_for_ideogram_image_mm = wikitext_for_ideogram_image_mm.."[[File:HSR 1996 II 3.5e.svg|"..arrowSign_width.."px|"..tooltip_arrowSign.."]]</div>"wikitext_for_ideogram_image_mm = wikitext_for_ideogram_image_mm.."<div style=\"position\: absolute\; left\: "..markerLocation_mm.."px\; top\: 19px\; padding\: 0\;\">[[File:Red rectangle "..markerWidth_mm.."x18.png|"..markerWidth_mm.."px|"..tooltip_arrowSign.."]]</div>"wikitext_for_ideogram_image_mm = wikitext_for_ideogram_image_mm.."</div>"wikitext_for_ideogram_image_mm = wikitext_for_ideogram_image_mm.."</div>"endroot: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(titleMouse):done() --end th:done() --end tr:tag('tr'):tag('td'):attr('colspan', '4'):css('text-align', 'center'):css('background-color', rowBGcolor):wikitext("[[File:Ideogram house mouse chromosome "..chr_mm..".svg|260px|"..chrText_mm.."]]"):done() --end td:done() --end tr:tag('tr'):tag('th'):attr('scope', 'row'):attr('width', '15%'):css('background-color', sideTitleBGcolor):wikitext(label_chr):done() --end th:tag('td'):attr('colspan', '3'):attr('width', '85%'):css('background-color', rowBGcolor):tag('span'):attr('class', 'plainlinks'):wikitext(chrText_mm..source_link_chr_mm):done() --end span :done() --end td:done() --end tr:tag('tr'):tag('td'):attr('colspan', '4'):css('text-align', 'center'):css('background-color', rowBGcolor):wikitext(wikitext_for_ideogram_image_mm):done() --end td:done() --end tr:tag('tr'):tag('th'):attr('scope', 'row'):attr('rowspan', '2'):attr('width', '15%'):css('background-color', sideTitleBGcolor):wikitext(label_locus):done() --end th:tag('td'):attr('rowspan', '2'):attr('width', '35%'):css('background-color', rowBGcolor):tag('span'):attr('class', 'plainlinks'):wikitext(cytoband_mm):done() --end span:done() --end td:tag('th'):attr('scope', 'row'):css('background-color', sideTitleBGcolor):wikitext(label_gstart):done() --end th:tag('td'):css('background-color', rowBGcolor):tag('span'):attr('class', 'plainlinks'):wikitext(p.separateWithComma(gstart_mm).." [[Base pair|bp]]"..source_link_gstart_mm):done() --end span :done() --end td:done() --end tr:tag('tr'):tag('th'):attr('scope', 'row'):css('background-color', sideTitleBGcolor):wikitext(label_gend):done() --end th:tag('td'):css('background-color', rowBGcolor):tag('span'):attr('class', 'plainlinks'):wikitext(p.separateWithComma(gend_mm).." [[Base pair|bp]]"..source_link_gend_mm):done() --end span :done() --end td:done() --end tr:done() --end table :done() --end td:done() --end trendendp.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 expand') :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 trendp.renderGeneOntology = function(mol_funct, cell_comp, bio_process, uniprotID)local title = "[[Gene_ontology|Gene ontology]]" --**lclz**local mol_funct_title = "Molecular function" --**lclz**local cell_comp_title = "Cellular component" --**lclz**local bio_process_title = "Biological process" --**lclz**local amigo_link = "[http://amigo.geneontology.org/" .. " Amigo]"local quickGO_link = "[https://www.ebi.ac.uk/QuickGO/" .. " QuickGO]"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') --create title bar :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') :css('background-color', sideTitleBGcolor) :wikitext(mol_funct_title) :done() --end th :tag('td') :css('background-color', rowBGcolor) :tag('span') :attr('class', 'plainlinks') :wikitext(mol_funct) :done() --end span :done() --end td :done() --end tr :tag('tr') :tag('th') :css('background-color', sideTitleBGcolor) :wikitext(cell_comp_title) :done() --end th :tag('td') :css('background-color', rowBGcolor) :tag('span') :attr('class', 'plainlinks') :wikitext(cell_comp) :done() --end span :done() --end td :done() --end tr :tag('tr') :tag('th') :css('background-color', sideTitleBGcolor) :wikitext(bio_process_title) :done() --end th :tag('td') :css('background-color', rowBGcolor) :tag('span') :attr('class', 'plainlinks') :wikitext(bio_process) :done() --end span :done() --end td :done() --end tr :tag('tr') :tag('td') :css('background-color', rowBGcolor) :css('text-align', 'center') :attr('colspan', '4') :wikitext("Sources:") :wikitext(amigo_link) :wikitext(" / ") :wikitext(quickGO_link) :done() --end td :done() --end tr:done() --end table:done() --end td:done() --end trend p.renderOrthologs = function(frame, entrez_gene, entrez_gene_mm, ensembl, ensembl_mm, uniprot, uniprot_mm, refseq_mRNA, refseq_mRNA_mm, refseq_prot, refseq_prot_mm, db, chr, gstart, gend, db_mm, chr_mm,gstart_mm, gend_mm) local title = "[[Ortholog|Orthologs]]" --**lclz**--to do make the list creation a function--create list for entrez idslocal category_chromosome = '[[Category:Genes on human chromosome '..chr..']]'-- *lclz*: Category nameif chr == "MT" thencategory_chromosome = '[[Category:Human mitochondrial genes]]'-- *lclz*: Category name for mtDNA genesendif mw.title.getCurrentTitle().namespace ~= 0 thencategory_chromosome = ""endlocal entrezTitle = "[[Entrez|Entrez]]"entrez_gene = string.gsub(entrez_gene, "%s", "")local entrez_link = "n/a"local entrez_collapse local entrez_default = ""local split_entrez = mw.text.split(entrez_gene, ",")local entrez_link_list = {}for k,v in ipairs(split_entrez) do if string.match(v, '%w+') and v ~= "n/a" thenentrez_link_list[#entrez_link_list+1] = "[https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=retrieve&dopt=default&list_uids="..entrez_gene.."&rn=1 "..entrez_gene.."]"endend--if less than 5 don't create collapsible listif table.getn(entrez_link_list) < 5 thenentrez_collapse = "none"if entrez_default == nil and table.getn(entrez_link_list) == 0 then entrez_link = "n/a" endelseentrez_collapse = "collapsible collapsed"entrez_default = table.remove(entrez_link_list, 1) .. '<br>' .. table.remove(entrez_link_list, 1) .. '<br>' ..table.remove(entrez_link_list, 1) .. '<br>' .. table.remove(entrez_link_list, 1) .. '<br>' .. table.remove(entrez_link_list, 1) .. '<br>'--get first 5 elements in table and use for displayendif entrez_link_list[#entrez_link_list] thenentrez_link = table.concat(entrez_link_list, "<br>")end--create list for mouse Entrez identrez_gene_mm = string.gsub(entrez_gene_mm, "%s", "")local entrez_mm_link = "n/a"local entrez_mm_collapse local entrez_mm_default = ""local split_entrez_mm = mw.text.split(entrez_gene_mm, ",")local entrez_mm_link_list = {}for k,v in ipairs(split_entrez_mm) do if string.match(v, '%w+') and v ~= "n/a" thenentrez_mm_link_list[#entrez_mm_link_list+1] = "[https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=retrieve&dopt=default&list_uids="..v.."&rn=1 "..v.."]"endend--if less than 5 don't create collapsible listif table.getn(entrez_mm_link_list) < 5 thenentrez_mm_collapse = "none"if entrez_mm_default == nil and table.getn(entrez_mm_link_list) == 0 then entrez_mm_link = "n/a" endelseentrez_mm_collapse = "collapsible collapsed"entrez_mm_default = table.remove(entrez_mm_link_list, 1) .. '<br>' .. table.remove(entrez_mm_link_list, 1) .. '<br>' ..table.remove(entrez_mm_link_list, 1) .. '<br>' .. table.remove(entrez_mm_link_list, 1) .. '<br>' .. table.remove(entrez_mm_link_list, 1) .. '<br>'--get first 5 elements in table and use for displayendif entrez_mm_link_list[#entrez_mm_link_list] thenentrez_mm_link = table.concat(entrez_mm_link_list, "<br>")end--create list of ensembl idlocal ensemblTitle = "[[Ensembl|Ensembl]]"ensembl = string.gsub(ensembl, "%s", "")local ensembl_link = "n/a"local ensembl_collapse local ensembl_default = ""local split_ensembl = mw.text.split(ensembl, ",")local ensembl_link_list = {}for k,v in ipairs(split_ensembl) do if string.match(v, '%w+') and v ~= "n/a" thenensembl_link_list[#ensembl_link_list+1] = "[http://www.ensembl.org/Homo_sapiens/geneview?gene="..v..";db=core".." "..v.."]"endend--if less than 5 don't create collapsible listif table.getn(ensembl_link_list) < 5 thenensembl_collapse = "none"if ensembl_default == nil and table.getn(ensembl_link_list) == 0 then ensembl_link = "n/a" endelseensembl_collapse = "collapsible collapsed"ensembl_default = table.remove(ensembl_link_list, 1) .. '<br>' .. table.remove(ensembl_link_list, 1) .. '<br>' ..table.remove(ensembl_link_list, 1) .. '<br>' .. table.remove(ensembl_link_list, 1) .. '<br>' .. table.remove(ensembl_link_list, 1) .. '<br>'--get first 5 elements in table and use for displayendif ensembl_link_list[#ensembl_link_list] thenensembl_link = table.concat(ensembl_link_list, "<br>")end--create list of mouse ensembl idlocal ensemblTitle = "[[Ensembl|Ensembl]]"ensembl_mm = string.gsub(ensembl_mm, "%s", "")local ensembl_mm_link = "n/a"local ensembl_mm_collapse local ensembl_mm_default = ""local split_ensembl_mm = mw.text.split(ensembl_mm, ",")local ensembl_mm_link_list = {}for k,v in ipairs(split_ensembl_mm) do if string.match(v, '%w+') and v ~= "n/a" thenensembl_mm_link_list[#ensembl_mm_link_list+1] = "[http://www.ensembl.org/Mus_musculus/geneview?gene="..v..";db=core".." "..v.."]"endend--if less than 5 don't create collapsible listif table.getn(ensembl_mm_link_list) < 5 thenensembl_mm_collapse = "none"if ensembl_mm_default == nil and table.getn(ensembl_mm_link_list) == 0 then ensembl_mm_link = "n/a" endelseensembl_mm_collapse = "collapsible collapsed"ensembl_mm_default = table.remove(ensembl_mm_link_list, 1) .. '<br>' .. table.remove(ensembl_mm_link_list, 1) .. '<br>' ..table.remove(ensembl_mm_link_list, 1) .. '<br>' .. table.remove(ensembl_mm_link_list, 1) .. '<br>' .. table.remove(ensembl_mm_link_list, 1) .. '<br>'--get first 5 elements in table and use for displayendif ensembl_mm_link_list[#ensembl_mm_link_list] thenensembl_mm_link = table.concat(ensembl_mm_link_list, "<br>")end--create lists of uniprot IDlocal uniprotTitle = "[[UniProt|UniProt]]"local uniprot_url = "https://www.uniprot.org/uniprot/"local uniprot_link = "n/a"local uniprot_collapselocal uniprot_default = ""--split string and loop through concatenate by <br>local split_uniprot = mw.text.split(uniprot, ",")local uniprot_link_list = {}local uniprot_first = {} --preferred values only display [O,P,Q] prefixed entries if they existlocal uniprot_alternate = {} --[A-N,R-Z] entrieslocal hash = {} --storage to look for duplicated values for k,v in ipairs(split_uniprot) do if not hash[v] then --only add if not found previously..some encodes uniprotID dup in different encodeslocal label = mw.text.trim(v)local concat_uniprot_link = uniprot_url .. labelif string.match(v, '%w+') and v ~= "n/a" thenif string.match(v, '^O') or string.match(v,'^P') or string.match(v, '^Q') then uniprot_first[#uniprot_first+1] = "[" .. concat_uniprot_link .. " " ..label .. "]"elseuniprot_alternate[#uniprot_alternate+1] = "[" .. concat_uniprot_link .. " " ..label .. "]"endendhash[v] = trueendend if table.getn(uniprot_first)>0 then --if there is something in the preferred values display else display anything elseuniprot_link_list = uniprot_firstelseuniprot_link_list = uniprot_alternateend--if less than 5 don't create collapsible listif table.getn(uniprot_link_list) < 5 thenuniprot_collapse = "none"if uniprot_default == nil and table.getn(uniprot_link_list) == 0 then uniprot_link = "n/a" endelseuniprot_collapse = "collapsible collapsed"uniprot_default = table.remove(uniprot_link_list, 1) .. '<br>' .. table.remove(uniprot_link_list, 1) .. '<br>' ..table.remove(uniprot_link_list, 1) .. '<br>' .. table.remove(uniprot_link_list, 1) .. '<br>' .. table.remove(uniprot_link_list, 1) .. '<br>'--get first 5 elements in table and use for displayendif uniprot_link_list[#uniprot_link_list] thenuniprot_link = table.concat(uniprot_link_list, "<br>")end --mouse uniprot listslocal uniprot_mm_link = "n/a"local uniprot_mm_collapselocal uniprot_mm_default = ""--split string and loop through concatenate by <br>local split_uniprot_mm = mw.text.split(uniprot_mm, ",") local uniprot_mm_link_list = {} local uniprot_mm_first = {} --preferred values only display [O,P,Q] prefixed entries if they exist local uniprot_mm_alternate = {} --[A-N,R-Z] entries local hash = {} --storage to look for duplicated valuesfor k,v in ipairs(split_uniprot_mm) do if not hash[v] then --only add if not found previously..some encodes uniprotID dup in different encodes local label = mw.text.trim(v) local concat_uniprot_link = uniprot_url .. label if string.match(v, '%w+') and v ~= "n/a" then if string.match(v, '^O') or string.match(v,'^P') or string.match(v, '^Q') then uniprot_mm_first[#uniprot_mm_first+1] = "[" .. concat_uniprot_link .. " " ..label .. "]"elseuniprot_mm_alternate[#uniprot_mm_alternate+1] = "[" .. concat_uniprot_link .. " " ..label .. "]"end endhash[v] = trueendendif table.getn(uniprot_mm_first)>0 then --if there is something in the preferred values display else display anything elseuniprot_mm_link_list = uniprot_mm_firstelseuniprot_mm_link_list = uniprot_mm_alternateend--if less than 5 don't create collapsible listif table.getn(uniprot_mm_link_list) < 5 thenuniprot__mm_collapse = "none"if uniprot_mm_default == nil and table.getn(uniprot_mm_link_list) == 0 then uniprot_mm_link = "n/a" endelseuniprot_mm_collapse = "collapsible collapsed"uniprot_mm_default = table.remove(uniprot_mm_link_list, 1) .. '<br>' .. table.remove(uniprot_mm_link_list, 1) .. '<br>' ..table.remove(uniprot_mm_link_list, 1) .. '<br>' .. table.remove(uniprot_mm_link_list, 1) .. '<br>' .. table.remove(uniprot_mm_link_list, 1) .. '<br>'--get first 5 elements in table and use for displayendif uniprot_mm_link_list[#uniprot_mm_link_list] thenuniprot_mm_link = table.concat(uniprot_mm_link_list, "<br>")endlocal ncbi_link = "https://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val="local refseq_mRNATitle = "RefSeq (mRNA)" -- *lclz*: sometimes--create list of links for refSeq mRNAlocal refseq_mRNA_link = "n/a"local refseq_mRNA_collapselocal refseq_mRNA_default = ""--split string and loop through concatenate by <br>local split_refseq_mRNA = mw.text.split(refseq_mRNA, ",")local link_list_first = {} --hold those the have NM or NP valueslocal link_list_alternate = {} --hold those that are XM or XP valueslocal link_list = {} --if NM,NP display if not display XM, XP values for k,v in ipairs(split_refseq_mRNA) dolocal label = mw.text.trim(v)local concat_ncbi_link = ncbi_link .. labelif string.match(v, '%w+') and v ~= "n/a" thenif string.match(v, 'NM') or string.match(v, 'NP') then link_list_first[#link_list_first+1] = "[" .. concat_ncbi_link .. " " ..label .. "]"elseif string.match(v, 'XM') or string.match(v, 'XP') thenlink_list_alternate[#link_list_alternate+1] = "[" .. concat_ncbi_link .. " " ..label .. "]"endend end if table.getn(link_list_first)>0 thenlink_list = link_list_firstelselink_list = link_list_alternateend--if less than 5 don't create collapsible listif table.getn(link_list) < 6 thenrefseq_mRNA_collapse = "none"if refseq_mRNA_default == nil and table.getn(link_list) == 0 then refseq_mRNA_link = "n/a" endelserefseq_mRNA_collapse = "collapsible collapsed"refseq_mRNA_default = table.remove(link_list, 1) .. '<br>' .. table.remove(link_list, 1) .. '<br>' ..table.remove(link_list, 1) .. '<br>' .. table.remove(link_list, 1) .. '<br>' .. table.remove(link_list, 1) .. '<br>'--get first 5 elements in table and use for displayendif link_list[#link_list] thenrefseq_mRNA_link = table.concat(link_list, "<br>")end--create list of links for refSeq mRNA for mouselocal refseq_mRNA_mm_link = "n/a"local refseq_mRNA_mm_collapselocal refseq_mRNA_mm_default = ""local split_refseq_mRNA_mm = mw.text.split(refseq_mRNA_mm, ",")local link_list_mm = {} --if NM,NP display if not display XM, XP valueslocal link_list_first = {} --hold those the have NM or NP valueslocal link_list_alternate = {} --hold those that are XM or XP values for k,v in ipairs(split_refseq_mRNA_mm) dolocal label = mw.text.trim(v)local concat_ncbi_link = ncbi_link .. labelif string.match(v, '%w+') and v ~= "n/a" thenif string.match(v, 'NM') or string.match(v, 'NP') then link_list_first[#link_list_first+1] = "[" .. concat_ncbi_link .. " " ..label .. "]"elseif string.match(v, 'XM') or string.match(v, 'XP') thenlink_list_alternate[#link_list_alternate+1] = "[" .. concat_ncbi_link .. " " ..label .. "]"endend endif table.getn(link_list_first)>0 thenlink_list_mm = link_list_firstelselink_list_mm = link_list_alternateend--if less than 5 don't create collapsible listif table.getn(link_list_mm) < 6 thenrefseq_mRNA_mm_collapse = "none"if refseq_mRNA_mm_default == nil and table.getn(link_list_mm) == 0 then refseq_mRNA_mm_link = "n/a" endelserefseq_mRNA_mm_collapse = "collapsible collapsed"refseq_mRNA_mm_default = table.remove(link_list_mm, 1) .. '<br>' .. table.remove(link_list_mm, 1) .. '<br>' ..table.remove(link_list_mm, 1) .. '<br>' .. table.remove(link_list_mm, 1) .. '<br>' .. table.remove(link_list_mm, 1) .. '<br>'--get first 5 elements in table and use for displayendif link_list_mm[#link_list_mm] thenrefseq_mRNA_mm_link = table.concat(link_list_mm, "<br>")end -- *lclz*: sometimeslocal refseq_protTitle = "RefSeq (protein)"--create list of links for human refseq proteinlocal refseq_prot_link = "n/a"local refseq_prot_collapse local refseq_prot_default = ""local split_refseq_prot = mw.text.split(refseq_prot, ",")local link_list_prot = {} local link_list_first = {} --hold those the have NM or NP valueslocal link_list_alternate = {} --hold those that are XM or XP valuesfor k,v in ipairs(split_refseq_prot) dolocal label = mw.text.trim(v)local concat_ncbi_link = ncbi_link .. labelif string.match(v, '%w+') and v ~= "n/a" thenif string.match(v, 'NM') or string.match(v, 'NP') then link_list_first[#link_list_first+1] = "[" .. concat_ncbi_link .. " " ..label .. "]"elseif string.match(v, 'XM') or string.match(v, 'XP') thenlink_list_alternate[#link_list_alternate+1] = "[" .. concat_ncbi_link .. " " ..label .. "]"endendendif table.getn(link_list_first)>0 thenlink_list_prot = link_list_firstelselink_list_prot = link_list_alternateend--if less than 5 don't create collapsible listif table.getn(link_list_prot) < 6 thenrefseq_prot_collapse = "none"if refseq_prot_default == nil and table.getn(link_list_prot) == 0 then refseq_prot_link = "n/a" endelserefseq_prot_collapse = "collapsible collapsed"refseq_prot_default = table.remove(link_list_prot, 1) .. '<br>' .. table.remove(link_list_prot, 1) .. '<br>' ..table.remove(link_list_prot, 1) .. '<br>' .. table.remove(link_list_prot, 1) .. '<br>' .. table.remove(link_list_prot, 1) .. '<br>'--get first 5 elements in table and use for displayend if link_list_prot[#link_list_prot] thenrefseq_prot_link = table.concat(link_list_prot, "<br>")end--create list of links for mouse refseq proteinlocal refseq_prot_mm_link = "n/a"local refseq_prot_mm_collapselocal refseq_prot_mm_default = ""local split_refseq_prot_mm = mw.text.split(refseq_prot_mm, ",")local link_list_prot_mm = {}local link_list_first = {} --hold those the have NM or NP valueslocal link_list_alternate = {} --hold those that are XM or XP values for k,v in ipairs(split_refseq_prot_mm) dolocal label = mw.text.trim(v)local concat_ncbi_link = ncbi_link .. labelif string.match(v, '%w+') and v ~= "n/a" thenif string.match(v, 'NM') or string.match(v, 'NP') then link_list_first[#link_list_first+1] = "[" .. concat_ncbi_link .. " " ..label .. "]"elseif string.match(v, 'XM') or string.match(v, 'XP') thenlink_list_alternate[#link_list_alternate+1] = "[" .. concat_ncbi_link .. " " ..label .. "]"endendendif table.getn(link_list_first)>0 thenlink_list_prot_mm = link_list_firstelselink_list_prot_mm = link_list_alternateend--if less than 5 don't create collapsible listif table.getn(link_list_prot_mm) < 6 thenrefseq_prot_mm_collapse = "none"if refseq_prot_mm_default == nil and table.getn(link_list_prot_mm) == 0 then refseq_prot_mm_link = "n/a" endelserefseq_prot_mm_collapse = "collapsible collapsed"refseq_prot_mm_default = table.remove(link_list_prot_mm, 1) .. '<br>' .. table.remove(link_list_prot_mm, 1) .. '<br>' ..table.remove(link_list_prot_mm, 1) .. '<br>' .. table.remove(link_list_prot_mm, 1) .. '<br>' .. table.remove(link_list_prot_mm, 1) .. '<br>'--get first 5 elements in table and use for displayendif link_list_prot_mm[#link_list_prot_mm] thenrefseq_prot_mm_link = table.concat(link_list_prot_mm, "<br>")endlocal locTitle = "Location (UCSC)" -- *lclz*local gstart_mb = p.locToMb(gstart, 2)local gend_mb = p.locToMb(gend, 2)local chr_loc_link = ""if (string.match(db, '%w+') and string.match(chr, '%w+') and string.match(gstart, '%w+') and string.match(gend, '%w+') )thenlocal chr_ucsc if chr == "MT" then chr_ucsc = "M" --UCSC uses "M" (not "MT") in URL for mitochondrial DNAelsechr_ucsc = chrendchr_loc_link = "[https://genome.ucsc.edu/cgi-bin/hgTracks?org=Human&db="..db.."&position=chr"..chr_ucsc..":"..gstart.."-"..gend.." ".."Chr "..chr_ucsc..": "..gstart_mb.." – "..gend_mb.." Mb]" elsechr_loc_link = "n/a"endlocal gstart_mm_mb = p.locToMb(gstart_mm, 2)local gend_mm_mb = p.locToMb(gend_mm, 2)local chr_loc_mm_link = ""if (string.match(db_mm, '%w+') and string.match(chr_mm, '%w+') and string.match(gstart_mm, '%w+') and string.match(gend_mm, '%w+') )thenlocal chr_mm_ucsc if chr_mm == "MT" then chr_mm_ucsc = "M" --UCSC uses "M" (not "MT") in URL for mitochondrial DNAelsechr_mm_ucsc = chr_mmendchr_loc_mm_link = "[https://genome.ucsc.edu/cgi-bin/hgTracks?org=Mouse&db="..db_mm.."&position=chr"..chr_mm_ucsc..":"..gstart_mm.."-"..gend_mm.." ".."Chr "..chr_mm_ucsc..": "..gstart_mm_mb.." – "..gend_mm_mb.." Mb]"elsechr_loc_mm_link = "n/a"endlocal pubmedTitle = "[[PubMed|PubMed]] search" -- *lclz*local pubmed_link = entrez_geneif string.match(entrez_gene, '%w+') and entrez_gene ~= "n/a" thenpubmed_link = frame:extensionTag("ref",frame:expandTemplate{ title = 'cite_web', args = { title ="Human PubMed Reference:" , url = "https://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=Link&LinkName=gene_pubmed&from_uid="..entrez_gene, website = "National Center for Biotechnology Information, U.S. National Library of Medicine" } } )--expandTemplate creates cite web template {{cite web|title=value|url=ref_link..ect}} endlocal pubmed_mm_link = entrez_gene_mmif string.match(entrez_gene_mm, '%w+') and entrez_gene_mm ~= "n/a" thenpubmed_mm_link = frame:extensionTag("ref",frame:expandTemplate{ title = 'cite_web', args = { title ="Mouse PubMed Reference:" , url ="https://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=Link&LinkName=gene_pubmed&from_uid="..entrez_gene_mm, website = "National Center for Biotechnology Information, U.S. National Library of Medicine" } } )--expandTemplate creates cite web template {{cite web|title=value|url=ref_link..ect}}endroot: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("Species") --**lclz** :done() --end th :tag('td') :wikitext("'''Human'''") --**lclz** :done() --end td :tag('td') :wikitext("'''Mouse'''") --**lclz** :done() --end td :done() --end tr :tag('tr') :tag('th') :attr('scope', 'row') :css('background-color', sideTitleBGcolor) :wikitext(entrezTitle) :done() --end th :tag('td') :tag('table') :attr('class', entrez_collapse) :css('padding', '0') :css('border', 'none') :css('margin', '0') :css('width', '100%') :css('text-align', 'right') :tag('tr') :tag('th') :attr('colspan', '1') :tag('span') :attr('class', 'plainlinks') :wikitext(entrez_default) :done() --end span :done() --end th :done() --end tr :tag('tr') :tag('td') :attr('colspan', '1') :tag('p') :attr('class', 'plainlinks') :wikitext(entrez_link) :done() --end p :done() --end td :done() --end tr :done() --end table :done() --end td:tag('td') :tag('table') :attr('class', entrez_mm_collapse) :css('padding', '0') :css('border', 'none') :css('margin', '0') :css('width', '100%') :css('text-align', 'right') :tag('tr') :tag('th') :attr('colspan', '1') :tag('span') :attr('class', 'plainlinks') :wikitext(entrez_mm_default) :done() --end span :done() --end th :done() --end tr :tag('tr') :tag('td') :attr('colspan', '1') :tag('p') :attr('class', 'plainlinks') :wikitext(entrez_mm_link) :done() --end p :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(ensemblTitle) :done() --end th :tag('td') :tag('table') :attr('class', ensembl_collapse) :css('padding', '0') :css('border', 'none') :css('margin', '0') :css('width', '100%') :css('text-align', 'right') :tag('tr') :tag('th') :attr('colspan', '1') :tag('span') :attr('class', 'plainlinks') :wikitext(ensembl_default) :done() --end span :done() --end th :done() --end tr :tag('tr') :tag('td') :attr('colspan', '1') :tag('p') :attr('class', 'plainlinks') :wikitext(ensembl_link) :done() --end p :done() --end td :done() --end tr :done() --end table :done() --end td:tag('td') :tag('table') :attr('class', ensembl_mm_collapse) :css('padding', '0') :css('border', 'none') :css('margin', '0') :css('width', '100%') :css('text-align', 'right') :tag('tr') :tag('th') :attr('colspan', '1') :tag('span') :attr('class', 'plainlinks') :wikitext(ensembl_mm_default) :done() --end span :done() --end th :done() --end tr :tag('tr') :tag('td') :attr('colspan', '1') :tag('p') :attr('class', 'plainlinks') :wikitext(ensembl_mm_link) :done() --end p :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(uniprotTitle) :done() --end th :tag('td') :tag('table') :attr('class', uniprot_collapse) :css('padding', '0') :css('border', 'none') :css('margin', '0') :css('width', '100%') :css('text-align', 'right') :tag('tr') :tag('th') :attr('colspan', '1') :tag('span') :attr('class', 'plainlinks') :wikitext(uniprot_default) :done() --end span :done() --end th :done() --end tr :tag('tr') :tag('td') :attr('colspan', '1') :tag('p') :attr('class', 'plainlinks') :wikitext(uniprot_link) :done() --end p :done() --end td :done() --end tr :done() --end table :done() --end td :tag('td') :tag('table') :attr('class', uniprot_mm_collapse) :css('padding', '0') :css('border', 'none') :css('margin', '0') :css('width', '100%') :css('text-align', 'right') :tag('tr') :tag('th') :attr('colspan', '1') :tag('span') :attr('class', 'plainlinks') :wikitext(uniprot_mm_default) :done() --end span :done() --end th :done() --end th :tag('tr') :tag('td') :attr('colspan', '1') :tag('p') :attr('class', 'plainlinks') :wikitext(uniprot_mm_link) :done() --end p :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(refseq_mRNATitle) :done() --end th :tag('td') --RNASeq mRNA collapsible table :tag('table') :attr('class', refseq_mRNA_collapse) :css('padding', '0') :css('border', 'none') :css('margin', '0') :css('width', '100%') :css('text-align', 'right') :tag('tr') :tag('th') :attr('colspan', '1') :attr('class', 'plainlinks') :wikitext(refseq_mRNA_default) :done() --end th :done() --end tr :tag('tr') :tag('td') :attr('colspan', '1') :tag('p') :tag('span') :attr('class', 'plainlinks') :wikitext(refseq_mRNA_link) :done() --end span :done() --end p :done() --end td :done() --end tr :done() --end table :done() --end td :tag('td') --RNASeq mRNA collapsible table for mouse :tag('table') :attr('class', refseq_mRNA_mm_collapse) :css('padding', '0') :css('border', 'none') :css('margin', '0') :css('width', '100%') :css('text-align', 'right') :tag('tr') :tag('th') :attr('colspan', '1') :attr('class', 'plainlinks') :wikitext(refseq_mRNA_mm_default) :done() --end th :done() --end tr :tag('tr') :tag('td') :attr('colspan', '1') :tag('p') :tag('span') :attr('class', 'plainlinks') :wikitext(refseq_mRNA_mm_link) :done() --end span :done() --end p :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(refseq_protTitle) :done() --end th :tag('td') --RNASeq protein collapsible table :tag('table') :attr('class', refseq_prot_collapse) :css('padding', '0') :css('border', 'none') :css('margin', '0') :css('width', '100%') :css('text-align', 'right') :tag('tr') :tag('th') :attr('colspan', '1') :attr('class', 'plainlinks') :wikitext(refseq_prot_default) :done() --end th :done() --end tr :tag('tr') :tag('td') :attr('colspan', '1') :tag('p') :tag('span') :attr('class', 'plainlinks') :wikitext(refseq_prot_link) :done() --end span :done() --end p :done() --end td :done() --end tr :done() --end table :done() --end td:tag('td') --RNASeq protein collapsible table for mouse :tag('table') :attr('class', refseq_prot_mm_collapse) :css('padding', '0') :css('border', 'none') :css('margin', '0') :css('width', '100%') :css('text-align', 'right') :tag('tr') :tag('th') :attr('colspan', '1') :attr('class', 'plainlinks') :wikitext(refseq_prot_mm_default) :done() --end th :done() --end tr :tag('tr') :tag('td') :attr('colspan', '1') :tag('p') :tag('span') :attr('class', 'plainlinks') :wikitext(refseq_prot_mm_link) :done() --end span :done() --end p :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(locTitle) :done() --end th :tag('td') :tag('span') :attr('class', 'plainlinks') :wikitext(chr_loc_link) :done() --end span :done() --end td :tag('td') :tag('span') :attr('class', 'plainlinks') :wikitext(chr_loc_mm_link) :done() --end span :done() --end td :done() --end tr :tag('tr') :tag('th') :attr('scope', 'row') :css('background-color', sideTitleBGcolor) :wikitext(pubmedTitle) :done() --end th :tag('td') :tag('span') :attr('class', 'plainlinks') :wikitext(pubmed_link) :done() --end span :done() --end td :tag('td') :tag('span') :attr('class', 'plainlinks') :wikitext(pubmed_mm_link) :done() --end span :wikitext(category_chromosome) :done() --end td :done() --end trendp.formatRow = function(title) root :tag('tr') :tag('td') :attr('colspan', '4') :css('text-align', 'center') :css('background-color', rowBGcolor) :tag('table') :css('padding', '0') :css('border', 'none') :css('margin', '0') :css('width', '100%') :css('text-align', 'left') :tag('tr') --create title header :css('background-color',titleBGcolor) :css('text-align', 'center') :tag('th') :attr('colspan',"2") :wikitext(title) :done() --end th :done() --end tr :done() --end table :done() --end td :done() --end trendp.renderFooter = function(Qid, Qid_mm) local text = "[[Wikidata|Wikidata]]" --**lclz** local hs_link = "[[d:"..Qid.."|View/Edit Human]]" --**lclz** local mm_link = "" local link_no_hs local link_no_mm if Qid_mm == "" then link_no_mm = 0 link_no_hs = 4 else link_no_mm = 2 link_no_hs = 2 mm_link = "[[d:"..Qid_mm.."|View/Edit Mouse]]" --**lclz** end root :tag('tr') :tag('td') :attr('colspan', '4') :css('text-align', 'center') :css('font-size','x-small') :css('background-color', rowBGcolor) :wikitext(text) :done() --end td :tag('tr') :tag('td') :attr('colspan', '4') :css('text-align', 'center') :css('font-size','x-small') :css('background-color', rowBGcolor) :tag('table') :css('padding', '0') :css('border', 'none') :css('margin', '0') :css('width', '100%') :css('text-align', 'center') :tag('tr') :tag('td') :attr('colspan', link_no_hs) :css('background-color', rowBGcolor) :css('text-align', 'center'):css('font-size','x-small'):wikitext(hs_link):done() --end td:tag('td') :attr('colspan', link_no_mm) :css('background-color', rowBGcolor) :css('text-align', 'center'):css('font-size','x-small'):wikitext(mm_link):done() --end td:done() --end tr:done() --end table:done() --end trroot:done() --end root tableend--this code isn't used was hoping could do some generalization of rowsp.rowLabel=function(label)root :tag('tr') :tag('th') :attr('rowspan', '2') :css('background-color', sideTitleBGcolor) :css('width', '43px') :wikitext(label) --:done()end-- look into entity objectp.getLabel = function(entity)local data = entitylocal f = {'labels','en','value'}local i = 1while true dolocal index = f[i]if not index thenif type(data) == "table" thenreturn mw.text.jsonEncode(data, mw.text.JSON_PRESERVE_KEYS + mw.text.JSON_PRETTY)elsereturn tostring(data)endenddata = data[index] or data[tonumber(index)]if not data thenreturnendi = i + 1endend--general function to get value given an entity and propertyp.getValue = function(entity, propertyID, return_val)local claimsif return_val == nil then return_val = "" end local sep = " " --could ad as input parameter if need beif entity and entity.claims thenclaims = entity.claims[propertyID]endif claims then-- if wiki-linked value output as link if possibleif (claims[1] and claims[1].mainsnak.snaktype == "value" and claims[1].mainsnak.datavalue.type == "wikibase-entityid") thenlocal out = {}for k, v in pairs(claims) dolocal datav = mw.wikibase.label("Q" .. v.mainsnak.datavalue.value["numeric-id"])if datav == nil then datav = " " end out[#out + 1] = datavendreturn table.concat(out, sep)else-- just return best valuesreturn entity:formatPropertyValues(propertyID).valueendelsereturn return_valendendp.getValueProtein = function(protein_entities, propertyID, return_val)if return_val == nil then return_val = "" endlocal sep = "," local overall_results = {} --should return empty if nothing assignedfor key, val in pairs(protein_entities) do --in cases where there are multiple encodes we loop through each and return concatenated data as a wholelocal claimslocal entity = val --each protein in encodesif entity and entity.claims thenclaims = entity.claims[propertyID]endif claims thenlocal results-- if wiki-linked value output as link if possibleif (claims[1] and claims[1].mainsnak.snaktype == "value" and claims[1].mainsnak.datavalue.type == "wikibase-entityid") thenlocal out = {}for k, v in pairs(claims) dolocal datav = mw.wikibase.label("Q" .. v.mainsnak.datavalue.value["numeric-id"])if datav == nil then datav = " " end out[#out + 1] = datavendresults = table.concat(out, sep)elseresults = entity:formatPropertyValues(propertyID).valueendoverall_results[#overall_results+1] = results --individual propertyID value stored in this indexendendlocal str_overall_results = table.concat(overall_results, sep) --weirdness happens when add a sep = " " otherwise each value represented one timeif string.match(str_overall_results, '%w+') thenreturn str_overall_results elsereturn return_valendend--general function to get value given an entity and propertyp.getQid = function(entity)local Qidif entity and entity.id thenQid = entity.idreturn Qidelsereturn ""endend--get random value that is preferred ranked -- *lclz*: Sometimes Wikibase returns punctuations other than "," depending on-- your site's language. Consider adding a gsub here.p.getRefseq_mRNA = function(entity, propertyID, return_val)if return_val == nil then return_val = "" endlocal input_rank = "RANK_PREFERRED" ---this is mostly like won't do anything because ranking isn't maintained in wikidata local claimsif entity.claims thenclaims = entity.claims[propertyID]endif claims then-- if wiki-linked value output as link if possibleif (claims[1] and claims[1].mainsnak.snaktype == "value" and claims[1].mainsnak.datavalue.type == "wikibase-entityid" ) thenlocal out = {}for k, v in pairs(claims) dolocal sitelink = mw.wikibase.sitelink("Q" .. v.mainsnak.datavalue.value["numeric-id"])local label = mw.wikibase.label("Q" .. v.mainsnak.datavalue.value["numeric-id"])if label == nil then label = "Q" .. v.mainsnak.datavalue.value["numeric-id"] endif sitelink thenout[#out + 1] = "[[" .. sitelink .. "|" .. label .. "]]"elseout[#out + 1] = "[[:d:Q" .. v.mainsnak.datavalue.value["numeric-id"] .. "|" .. label .. "]]"endendreturn table.concat(out, ", ")elselocal results = entity:formatPropertyValues(propertyID, mw.wikibase.entity.claimRanks).value --loop through results until get a NP or NM or just return whatever is in first element--[[local results_split = mw.text.split(results, ",")local preffered_results = " "if results_split[1] thenpreferred_result = mw.text.trim(results_split[1]) --return first element if desired prefix not found and remove whitespaceendlocal id --refseq id in questionfor i, id in ipairs(results_split) dolocal trim_id = mw.text.trim(id) if string.match( trim_id, '^NM_%d+') then preferred_result = trim_id --overwrite each time found only need one to display endendif preferred_result thenreturn preferred_result --return a id starting with NP or NMelsereturn return_val --return first element because desired prefix not found and remove whitespacesend--]]return resultsendelsereturn return_valendend-- *lclz*: same as getRefseq_mRNAp.getRefseq_protein = function(protein_entities, propertyID, return_val)local sep = ","local overall_results = {} --should return empty if nothing assignedfor key, val in pairs(protein_entities) do --in cases where there are multiple encodes we loop through each and return concatenated data as a wholelocal claimslocal entity = val --each protein in encodesif entity.claims thenclaims = entity.claims["P637"]endif claims thenlocal results-- if wiki-linked value output as link if possibleif (claims[1] and claims[1].mainsnak.snaktype == "value" and claims[1].mainsnak.datavalue.type == "wikibase-entityid" ) thenlocal out = {}for k, v in pairs(claims) dolocal datav = mw.wikibase.label("Q" .. v.mainsnak.datavalue.value["numeric-id"])if datav == nil then datav = " " end out[#out + 1] = datavendresults = table.concat(out, sep)elseresults = entity:formatPropertyValues("P637", mw.wikibase.entity.claimRanks).value endoverall_results[#overall_results+1] = results --a list is in each index endend--why are there duplicate results herelocal str_overall_results = table.concat(overall_results, sep)return str_overall_resultsend--[[local results_split = mw.text.split(str_overall_results, sep) --split complete list so can loop through..probably a more direct way to do this--loop through results until get a NP or NM or just return whatever is in first elementlocal preffered_result = results_split[1] or ""for i, id in ipairs(results_split) dolocal trim_id = mw.text.trim(id)--check of id starts with NP or NMif string.match( trim_id, '^NP_%d+') then preferred_result = trim_id --overwrite each time found only need one to displayendend--check if something in preffered_result if not get first element in result_splitif p.isempty(preffered_result) thenreturn return_valelsereturn preferred_result --return a id starting with NP or NMendend --]]--gets an imagep.getImage = function(entity, propertyID, sep, imgsize) local claims if entity and entity.claims then claims = entity.claims[propertyID] end if claims then if (claims[1] and claims[1].mainsnak.datatype == "commonsMedia") then local out = {} for k, v in pairs(claims) do local filename = v.mainsnak.datavalue.value out[#out + 1] = "[[File:" .. filename .. "|" .. imgsize .. "]]" end return table.concat(out, sep) else return "" end else return "" end endp.getPDB = function(protein_entities)local pdb_propertyID = "P638"local overall_results = {}for key, val in pairs(protein_entities) do --in cases where there are multiple encodes we loop through each and return concatenated data as a wholelocal claimslocal entity = valif entity and entity.claims thenclaims = entity.claims[pdb_propertyID]endlocal sitelink = "https://www.rcsb.org/structure/"if claims thenlocal resultsif (claims[1] and claims[1].mainsnak.snaktype == "value") thenlocal out = {}for k, v in pairs(claims) dolocal label = mw.wikibase.label(v.mainsnak.datavalue.value)if label == nil then label = v.mainsnak.datavalue.value endif sitelink thenout[#out + 1] = "[" .. sitelink .. label .. " " ..label .. "]"elseout[#out + 1] = "[[:d:Q" .. v.mainsnak.datavalue.value .. "|" .. label .. "]]"endendresults = table.concat(out, ", ") -- *lclz*: punctuation (CJK comma, etc.)elseresults = entity:formatPropertyValues(propertyID, mw.wikibase.entity.claimRanks).valueendoverall_results[#overall_results+1] = results --individual propertyID values stored in this indexendendreturn table.concat(overall_results, ",%%s")endfunction p.getAliases(entity)a = ''if entity['aliases'] ~= nil then-- *lclz*: You will need a different language here.-- If you are aiming for an "en" fallback, consider a set data structure.-- zhwp went a bit further here: they moved this call after "gene_symbol",-- so that this function can perform the deduplication here instead of-- in renderIdentifiers. That way they skip messing with commas and spaces. local test = entity['aliases']['en'] if test thenfor key, value in ipairs(test) doa = a .. ', ' .. value['value']endreturn aelsereturn ""endelsereturn ""endend--get a geneome start P644 or end P645p.getChromosomeLoc = function(entity, propertyID, prefix)-- will contain the numeric value for the requested coordinatelocal output = ""local sep = " "-- can only be P644 (genomic start) or P645 (genomic end) for this to work-- should probably try to catch that. Might also increase legibility to use specific variable names when possible--local propertyID = mw.text.trim(frame.args[1] or "") -- this can really only be P659 right now. I'm not sure of the value of including it as a parameter as other values will likely break this functionlocal qualifierID = "P659" --mw.text.trim(frame.args[2] or "")-- Why do we include this here? What should happen if FETCH_WIKIDATA is not included? --local input_parm = mw.text.trim(frame.args[3] or "")-- this can needs to be fed to the function either by a call to {{#invoke:Wikidata|pageId}} or by setting it directly (e.g. if the function was applied on a page other than the targeted gene)--alert if this id is not a valid thing in wikidata, a Lua error will occur that says--The ID entered is unknown to the system. Please use a valid entity ID.--local itemID = mw.text.trim(frame.args[4] or "")-- will track the different builds pulled from the qualifierslocal newest_build = "0"-- starts the process--local entity = mw.wikibase.getEntityObject(itemID)local claims--gets a table of claims on the (genomic start or end) property Q19847637if entity and entity.claims thenclaims = entity.claims[propertyID]end--will return nothing if no claims are foundif claims then--checking to be sure claims is populated, not sure it its neededif (claims[1] ) then--useful for debugging--local out = {}--pulls the genome location from the claimfor k, v in pairs(claims) dolocal location = v.mainsnak.datavalue.value--debugging--out[#out + 1] = k.." location:" .. location.. " || " --gets the qualifiers linked to the current claimlocal quals if v.qualifiers thenquals = v.qualifiers.P659end--if there are anyif quals thenfor qk, qv in pairs(quals) dolocal qual_obj_id = "Q"..qv.datavalue.value["numeric-id"]--get to the entity targeted by the qualifier property. Genome builds are Items in wikidatalocal qual_obj = mw.wikibase.getEntityObject(qual_obj_id)local alias = ""--this uses the aliases to pull out version numbers--seems like there ought to be a better way to do this, but likely would need to change the data added by the botif qual_obj["aliases"] ~= nil thenlocal test = qual_obj["aliases"]["en"]for key, value in ipairs(test) doif string.match(value['value'], prefix) thenalias = value['value']local build_no = alias:gsub(prefix,"")--report only the most location associated with the most recent build--if there is more than one location per build, just give one back as that is not our problem right now.if build_no > newest_build thenoutput = locationnewest_build = build_noendendendendend--in case there are no qualifiers, but there is a location, might as well return itelse output = location endendreturn outputelsereturn ""endelsereturn ""--debug--"no claims for "..itemID.." prop "..propertyIDendendp.getAliasFromGenomeAssembly = function(entity, prefix)-- will contain the numeric value for the requested coordinatelocal output = ""local sep = " "local propertyID = "P644" --genomic start used local qualifierID = "P659" --genomic assemblylocal newest_build = "0"local claimsif entity.claims then claims = entity.claims[propertyID]end--will return nothing if no claims are foundif claims then--checking to be sure claims is populated, not sure it its neededif (claims[1] ) then--useful for debugging--local out = {}--pulls the genome location from the claimfor k, v in pairs(claims) dolocal qualsif v.qualifiers thenquals = v.qualifiers.P659end--if there are any--as of Aug. 2017, P659-genomic assembly is stored only in human genomic data. GRCh38 (newer) or GRCh37(older).--Mouse genomic data doesn't have P659-genomic assembly data. But mouse has only one version. GRCm38/mm10.if quals thenfor qk, qv in pairs(quals) dolocal qual_obj_id = "Q"..qv.datavalue.value["numeric-id"]--get to the entity targeted by the qualifier property. Genome builds are Items in wikidatalocal qual_obj = mw.wikibase.getEntityObject(qual_obj_id)local alias = ""--this uses the aliases to pull out version numbers--seems like there ought to be a better way to do this, but likely would need to change the data added by the botif qual_obj["aliases"] ~= nil thenlocal test = qual_obj["aliases"]["en"]for key, value in ipairs(test) doif string.match(value['value'], prefix) thenalias = value['value']local build_no = alias:gsub(prefix,"")--For example, prefix is "hg" (this is set when the function was called),--alias is "hg38" (which is data stored in Wikidata). Then "build_no" becomes "38".--report only the most location associated with the most recent build--if there is more than one location per build, just give one back as that is not our problem right now.if build_no > newest_build thennewest_build = build_noendendendendend--in case there are no qualifiers, but there is a location, might as well return itelse output = location endendreturn prefix..newest_buildelsereturn ""endelsereturn ""endend-- *lclz*: Your language's wikidata may have different nouns for chromosome and-- mitochodria.p.trimChromosome = function(entity)local string_to_trim = p.getValue(entity, "P1057")local out = ''--"mitochondrion" and "chromosome MT" is used for mitochondrial DNA.--See [[d:Special:WhatLinksHere/Q18694495]]if string.find(string_to_trim, 'chromosome MT') or string.find(string_to_trim, 'mitochondri') then --match both 'mitochondrio'/'mitochondrial'out = "MT"elseif string.find(string_to_trim, 'chromosome') thenout = string.match(string_to_trim, "%d+")--extract number from stringif out == nil thenout = string.match(string_to_trim, "X") or string.match(string_to_trim, "Y")endendreturn outendp.locToMb = function(num, idp) num = tonumber(num) if num == nil then return "" else local mb = num/1000000 local mult = 10^(idp or 0) return math.floor(mb * mult + 0.5) / mult endendp.isempty = function(s) return s == nil or s == ''endp.getGO = function(protein_entities, propertyID)--propertyID ie molecular, cellular, functionlocal overall_results = {}local results = "" --string to returnfor key, val in pairs(protein_entities) dolocal claimslocal entity = valif entity.claims thenclaims = entity.claims[propertyID] -- ie molecular, cellular, functionendlocal propertyID_child = "P686" -- Gene Ontology IDif claims thenif (claims[1] and claims[1].mainsnak.snaktype == "value" and claims[1].mainsnak.datavalue.type == "wikibase-entityid") then--local out = {}for k, v in pairs(claims) dolocal itemID_child = "Q" .. v.mainsnak.datavalue.value["numeric-id"] --get Qid of property item so can get the GOidlocal entity = mw.wikibase.getEntityObject(itemID_child)local claimslocal result_GOID = ''if entity and entity.claims then claims = entity.claims[propertyID_child] endif claims thenresult_GOID = entity:formatPropertyValues(propertyID_child, mw.wikibase.entity.claimRanks).valueelseresult_GOID = nil --no GO IDendlocal sitelink = "http://amigo.geneontology.org/amigo/term/"local label = mw.wikibase.label("Q" .. v.mainsnak.datavalue.value["numeric-id"])if label == nil then label = "Q" .. v.mainsnak.datavalue.value["numeric-id"] endlocal wiki_link= ""if sitelink and result_GOID ~= nil thenwiki_link = "<big>•</big> [" .. sitelink .. result_GOID .. " " .. label .."]<br>"elsewiki_link = "<big>•</big> [[:d:Q" .. v.mainsnak.datavalue.value["numeric-id"] .. "|" .. label .. "]]<br>"endoverall_results[#overall_results+1] = wiki_linkendelseresults = entity:formatPropertyValues(propertyID, mw.wikibase.entity.claimRanks).valueendend--overall_results[#overall_results+1] = results --each protein GO terms stored in this index, so table contains all the GO terms with duplicates endlocal hash = {} --temp checklocal res = {} --no dupsfor _,v in ipairs(overall_results) do if (not hash[v]) then res[#res+1] = v hash[v] = true endendreturn table.concat(res, "")endlocal function getReference(qID, entity, property_id, ref_index)local f = {"claims",property_id, ref_index, "references"} local id = qID--if id and (#id == 0) then--id = nil--endlocal data = entityif not data thenreturn nilend local i = 1while true dolocal index = f[i]if not index thenif type(data) == "table" thenreturn mw.text.jsonEncode(data, mw.text.JSON_PRESERVE_KEYS + mw.text.JSON_PRETTY)elsereturn tostring(data)endenddata = data[index] or data[tonumber(index)]if not data thenreturn ""endi = i + 1endendp.getDisease= function(entity, propertyID) local claimsif return_val == nil then return_val = "" endif entity and entity.claims thenclaims = entity.claims[propertyID]endif claims then-- if wiki-linked value output as link if possibleif (claims[1] and claims[1].mainsnak.snaktype == "value" and claims[1].mainsnak.datavalue.type == "wikibase-entityid") thenlocal out = {}local datasource = {}--{{#invoke:Wikidata |ViewSomething |id=Q18023174 |claims|P2293|1|references|1|snaks|P854|1|datavalue|value}}--maybe there is a more direct way to find this than looping through the json objectfor k, v in pairs(claims) dolocal datav = mw.wikibase.label("Q" .. v.mainsnak.datavalue.value["numeric-id"])if datav == nil then datav = " " end local id = "Q" .. v.mainsnak.datavalue.value["numeric-id"]local linkTarget = mw.wikibase.sitelink(id)local refLink = ""local ref = ""ref = getReference("", entity, "P2293", k)if (ref ~= nil and ref ~= '') then --refLink = refLink..","..ref refLink = refend --if refLink = "" then --skip if there isn't a reference foundif linkTarget thenout[#out + 1] = "[["..linkTarget.."|"..datav.."]]"elseout[#out + 1] = "[[:d:" .. id .. "|" .. datav .. "]]"enddatasource[#out] = refLink--endendreturn out, datasourceelse-- just return best values--return entity:formatPropertyValues(propertyID).valuereturn return_val, return_valendelsereturn return_valend return return_valendp.getDrug= function(protein_entities, propertyID) local out = {}local datasource = {}local pname = {}local pqid = {}for key, val in pairs(protein_entities) dolocal claimslocal entity = vallocal name = check_values(p.getLabel,{entity})if entity.claims thenclaims = entity.claims[propertyID] -- ie physically interacts withendlocal protein_idif entity then protein_id = entity.id else protein_id = "" endif claims thenif (claims[1] and claims[1].mainsnak.snaktype == "value" and claims[1].mainsnak.datavalue.type == "wikibase-entityid") thenfor k, v in pairs(claims) dolocal datav = mw.wikibase.label("Q" .. v.mainsnak.datavalue.value["numeric-id"])if datav == nil then datav = "" endlocal id = "Q" .. v.mainsnak.datavalue.value["numeric-id"]local linkTarget = mw.wikibase.sitelink(id)local refLink = ""local ref = getReference(protein_id, entity, "P129",k) --just check if anything returnedif (ref ~= nil and ref ~= '') then refLink = ref endif linkTarget then out[#out + 1] = "[["..linkTarget.."|"..datav.."]]" else out[#out + 1] = "[[:d:" .. id .. "|" .. datav .. "]]" endpname[protein_id] = name pqid[#out] = protein_iddatasource[#out] = refLinkend --end k,v claims loopend --end claims[1]end --if claims end -- end protein_entities loopreturn out, datasource, pqid, pnameendp.separateWithComma= function(bp)--Separate number with comma. For example when this function gets "12345678", returns "12,345,678" local commaSeparated = bp while true do commaSeparated, k = string.gsub(commaSeparated, "^(-?%d+)(%d%d%d)", '%1,%2') if (k==0) then break end end return commaSeparatedendreturn p🔥 Top keywords: විශේෂ:ගවේෂණයකාලස් පුයිජ්දෙමොන්මුල් පිටුවඅධ්යාපනයවිශේෂ:මෑත වෙනස්වීම්සූනන් ඇඟ වැටීමේ ඵලාඵලවිකිපීඩියා:Contact usදුටුගැමුණු රජසාර ධර්මසාහිත්යයසීගිරියසිංහල සාහිත්යයසංස්කෘතියගෝලීයකරණයඅනගාරික ධර්මපාලපරිසර දූෂණයකුමාරතුංග මුනිදාසශ්රී දළදා මාළිගාවශ්රි ලංකාවේ පාසල් ලැයිස්තුවඑස්. මහින්ද හිමිශ්රී ලංකාවේ ප්රාදේශීය ලේකම් කොට්ඨාසශ්රී ලංකා පොලිස් සේවයශ්රී ලංකාවමාර්ටින් වික්රමසිංහරුවන්වැලිසෑයලිංගික සංසර්ගික ඉරියව්වොලිබෝල්ලිංගික සංසර්ගයවිකිපීඩියා:Administrators' noticeboardසාකච්ඡාව:මුල් පිටුවමනෝ විශ්ලේෂණවාදයසාමයපාසල්ස්ත්රී ස්වයං වින්දනයස්වයං වින්දනයළමා අපයෝජනයඅපරාධකළමනාකරණයපළමුවන විජයබාහු රජ