Module:Infobox gene: Difference between revisions

Revision as of 11:52, 18 April 2024

Revision as of 12:01, 24 May 2024

Line 20:

return("'''VALUE_ERROR''' (" .. tostring(val) .. ")")

end

end

local function trim(s)

return (s:gsub("^%s*(.-)%s*$", "%1"))

end

Line 49 ⟶ 53:

entity = mw.wikibase.getEntity()

if entity then root_qid = entity.id else root_qid = "" end

else

--assuming we think its good make one call to retrieve and store its wikidata representation

Line 135 ⟶ 138:

claims = entity_mouse.claims[protein_propertyID]

end

if claims then

ifand (claims[1]
and claims[1].mainsnak.snaktype == "value"
and claims[1].mainsnak.datavalue.type == "wikibase-entityid")
then

for k, v in pairs(claims) do

local 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)

end

end --will return nothing if no claims are found

end

end

Line 196 ⟶ 200:

p.renderImage(image)

p.renderAvailableStructures(uniprotID_hs, uniprotID_mm, checkOrtholog, pdbIDs) --PDB info

p.renderIdentifiers(aliases, hgnc_id, gene_symbol, homologene_id, omim_id, mgi_id, ChEMBL_id, IUPHAR_id, ec_no, entrez_gene, ensembl)

--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

Line 308 ⟶ 312:

local PDBe_list = " " --create a list with " or " if there is more than one uniprot

--get first uniprot in a list

if url_uniprot:match("([^,]+),") then --first check if there is a list if not just assume one value

PDBe_list = string.gsub(url_uniprot, ",", "%%20or%%20") --add or's inststead of commas

else

Line 399 ⟶ 403:

end

function p.renderIdentifiers(aliases, hgnc_id, gene_symbol, homologene_id, omim_id, mgi_id, ChEMBL_id, IUPHAR_id, ec_no, entrez_gene, ensembl)

local title = "Identifiers" --**lclz**

local label_aliases = "[[Gene nomenclature|Aliases]]" --**lclz**

Line 405 ⟶ 409:

if gene_symbol == "" or gene_symbol == nil then

symbol_url = ""

if elseif hgnc_id == "" or hgnc_id == nil then

symbol_url = gene_symbol

else

symbol_url = "[https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/"..hgnc_id.." "..gene_symbol.."]"

if hgnc_id == "" or hgnc_id == nil then

symbol_url = gene_symbol

else

symbol_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.aliases: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 end

local label_ext_id = "External IDs" --**lclz**

omim_id = string.gsub(omim_id, "%s", "")

local omim_list = mw.text.split(omim_id, localSeparatorStr)

Line 433:

end

end

omim = trim(string.gsub(omim, ", $"," ")) --remove comma from end

homologene_id = string.gsub(homologene_id, "%s", "")

local homolo_list = mw.text.split(homologene_id, localSeparatorStr)

Line 446 ⟶ 445:

end

end

homolo = trim(string.gsub(homolo, ", $"," ")) --remove comma from end

local 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, localSeparatorStr)

Line 463 ⟶ 460:

end

end

mgi = trim(string.gsub(mgi, ", $"," ")) --remove comma from end

local ChEMBL = ""

if string.match(ChEMBL_id, '%w+') then

Line 471 ⟶ 467:

local 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**

Line 477 ⟶ 473:

ec_no = string.gsub(ec_no, "%d%.%d+%.%d+%.%-", "")--remove those with"-" not in list

local link_ec_no = string.gsub(ec_no, "," ,"+") --create format for link

local EC = "[https://www.genome.jp/dbget-bin/www_bget?enzyme+" .. link_ec_no .. " " .. ec_no .. "]"

local oma = "[[Orthologous_MAtrix|OMA]]:"

oma = oma.."[https://omabrowser.org/oma/vps/"..mw.text.split(ensembl,",")[1].." "..gene_symbol.." - orthologs]"

external_id_table = {omim, mgi, homolo, ChEMBL, IUPHAR, genecards, oma}

external_id_processed_table = {}

for i, v in ipairs(external_id_table) do

if chr(v =~= "") then

external_id_processed_table[#external_id_processed_table + 1] = v

end

end

external_ids = tostring(table.concat(external_id_processed_table, "; "))

root

:tag('tr')

Line 522 ⟶ 526:

:tag('span')

:attr('class', 'plainlinks')

:wikitext(omimexternal_ids)

:wikitext(mgi)

:wikitext(homolo)

:wikitext(ChEMBL)

:wikitext(IUPHAR)

:wikitext(genecards)

:done() --end span

:done() --end td

Line 1,125 ⟶ 1,124:

function p.renderRNAexpression(expression_images, entrez_gene,

ensembl, bgee_expression, ensembl_mouse, bgee_expression_mouse)

local bgee_gene_page = "https://www.bgee.org/gene/"

local title = "[[Gene expression|RNA expression]] pattern" --**lclz**

local biogps_link = ""

Line 1,139 ⟶ 1,138:

local ensembl_id_mouse = string.match(ensembl_mouse,"%a+%d+") or ""

local bgee_title = "Bgee"

bgee_title = "[https://www.bgee.org/ " .. bgee_title .. "]"

local bgee_default = "["..bgee_gene_page..ensembl_id.." Top expressed in]"

bgee_expression = p.renderExpressionList(bgee_expression, bgee_default)

Line 1,423 ⟶ 1,422:

if chr == "MT" then

category_chromosome = '[[Category:Human mitochondrial genes]]'-- *lclz*: Category name for mtDNA genes

end

if chr == "" then

category_chromosome = '[[Category:Human genes]]' -- Per [[Wikipedia:Categories for discussion/Log/2023 August 15]]

end

if mw.title.getCurrentTitle().namespace ~= 0 then