Module:Infobox gene: Difference between revisions

Revision as of 06:49, 6 January 2017

Revision as of 01:02, 21 January 2017

Line 15:

end

--texts relevant to localization is tagged with --**lclz**

--on a page {{#invoke:Sandbox/genewiki/alllua|getTemplateData|QID=Q14865053}}

--in debug window

Line 259:

p.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='

Line 370:

p.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 = "[https://en.wikipedia.org/wiki/Human_Genome_Organisation Aliases]" --**lclz**

local symbol_url

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

Line 389:

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", "")

Line 523:

p.renderDiseases = function(frame, disease, dis_ref, name, qid)

local title = "Genetically Related Diseases" --**lclz**

--check first to see if any of the diseases have references

Line 643:

p.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]"

Line 729:

p.renderRNAexpression = function(expression_images, entrez_gene)

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

local biogps_link = "[http://biogps.org/gene/"..entrez_gene.."/ More reference expression data]" --**lclz**

root

:tag('tr')

Line 762:

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 = "Orthologs" --**lclz**

--to do make the list creation a function

--create list for entrez ids

Line 1,164:

: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

Line 1,556:

p.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

Line 1,568:

link_no_mm = 2

link_no_hs = 2

mm_link = "[[d:"..Qid_mm.."|View/Edit Mouse]]" --**lclz**

end