モジュール:Infobox gene

local p = { }
local navbar = require('Module:Navbar')._navbar
local infobox = require('Module:Infobox3cols').infobox
local infoboxImage = require('Module:InfoboxImage').InfoboxImage
-- wrapped "protected call", return "value error" with error info on error
local function check_values(f,args)
	    --local u= table.upack(args)
		local exist, val = pcall(f, unpack(args))
		if exist and val ~= nil then
			return(val)
		else
			-- Leaking some debugging info won't hurt....
			return("VALUE_ERROR (" .. tostring(val) .. ")")
		end
end
--texts relevant to localization are tagged with --**lclz*--on a page 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 page
	local root_qid = mw.text.trim(frame.args'QID'  or "") --try to get it from the args
	local mm_qid = ""
	--pull all the entity objects that we will need
	local	entity = {} 
	local	entity_protein = {}
	local	entity_mouse = {}
	local	entity_mouse_protein = {}
	local	checkOrtholog = "" --flag used to see if mouse data avaliable
	
	local mouse_propertyID = "P684" --actually ortholog property additional orthologs can exist
	local protein_propertyID = "P688" 
	--get root gene entity
	if root_qid == "" then
		entity = mw.wikibase.getEntityObject()
		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
		entity = mw.wikibase.getEntity(root_qid)
	end
	
	--need to figure out if it is protein or gene here
	local subclass = p.getValue(entity, "P31") or ""
	if string.find(subclass, 'タンパク質') then --if protein switch entity to gene
		if entity.claims then
	 		claims = entity.claims"P702" --encoded by
	 	end
		if claims then
			--go through each index and reassign entity
			entity = {}
			if (claims1 and claims1.mainsnak.snaktype == "value" and claims1.mainsnak.datavalue.type == "wikibase-entityid") then
				for k, v in pairs(claims) do --this would be problematic if multiple genes for the protein
					local itemID = "Q" .. claims#entity + 1.mainsnak.datavalue.value"numeric-id"
					entity#entity + 1 = mw.wikibase.getEntity(itemID)
					root_qid = itemID
				end
				
			end --will return nothing if no claims are found
		end
		 entity = mw.wikibase.getEntity(root_qid) 	
	 end
	
	
	--get the other related entities
	if entity then
		local claims = ""
	 	--get protein entity object
	 	if entity.claims then
	 		claims = entity.claimsprotein_propertyID
	 	end
		if claims then
			--go through each index and then make entity_protein indexed
			if (claims1 and claims1.mainsnak.snaktype == "value" and claims1.mainsnak.datavalue.type == "wikibase-entityid") then
				for k, v in pairs(claims) do
					local protein_itemID = "Q" .. claims#entity_protein + 1.mainsnak.datavalue.value"numeric-id"
					entity_protein#entity_protein + 1 = mw.wikibase.getEntity(protein_itemID)
				end
				
			end --will return nothing if no claims are found
		end
	
	 	--get mouse entity object
	 	if entity.claims then
			claims = entity.claimsmouse_propertyID
		end
		local qualifierID = "P703" --found in taxon
	local mouse_tax = "ハツカネズミ"
	if claims then
			if (claims1 and claims1.mainsnak.snaktype == "value" and claims1.mainsnak.datavalue.type == "wikibase-entityid") then
				for k, v in pairs(claims) do
				  	local mouse_itemID = "Q" .. v.mainsnak.datavalue.value"numeric-id"
					local quals 
					if v.qualifiers then
						quals = v.qualifiers.P703
					end
					if quals then
						for qk, qv in pairs(quals) do
							--get the taxon name in qualifier
							local qual_obj_id = "Q"..qv.datavalue.value"numeric-id"
							mw.wikibase.label(qual_obj_id)
							local qual_obj = mw.wikibase.label(qual_obj_id)
							if string.match(qual_obj, mouse_tax) then --check if this is mouse or other
								mm_qid = mouse_itemID 
								entity_mouse = mw.wikibase.getEntity(mouse_itemID)
								checkOrtholog = 1
							end
						end
					end
				end
			end --will return nothing if no claims are found
		else
			checkOrtholog = 0
		end
	
	 	--get mouse protein entity object
	 	if entity_mouse and entity_mouse.claims then
			claims = entity_mouse.claimsprotein_propertyID
		end
	 	if claims then
	 		if (claims1 and claims1.mainsnak.snaktype == "value" and claims1.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
	
	
	if entity then --only require the main gene entity
		--a list variables of all the data in the info box
		local 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 size
		local 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","","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 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 db_mm = check_values(p.getAliasFromGenomeAssembly, {entity_mouse,"mm"})
		local chr_mm = check_values( p.trimChromosome, {entity_mouse})
		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" } end
		if 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 Scheme
		rowBGcolor = '#eee'
		titleBGcolor = '#ddd'
		sideTitleBGcolor = '#c3fdb8'
		p.createTable()
	p.renderUpperTitle(name)
	--p.renderCaption()
	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)
		--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)
	--end
		
		if (chr ~= "" and gstart ~= "" and gend ~= "") or (chr_mm ~= "" and gstart_mm ~= "" and gend_mm ~= "") then
			p.renderGeneLocation(frame, chr, gstart, gend, db, ensembl, chr_mm, gstart_mm, gend_mm, db_mm, ensembl_mm, name)
		end
		if expression_images ~= ""  then
			p.renderRNAexpression(expression_images, entrez_gene)
		end
		if (mol_funct ~= "" and cell_comp ~= "" and bio_process ~= "") then
			p.renderGeneOntology(mol_funct, cell_comp, bio_process, uniprotID_hs)
		end
		p.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"
	end	
end
p.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')
end
end
--Title above image
p.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 tr
end
--This is a place holder for the image caption, which is stored in wikicommons comments unsure how to access 
p.renderCaption = function(entity)
	--caption
end
--gets default image
p.renderImage = function(image)
	root
			:tag('tr')
		:tag('td')
					:attr('colspan', 4)
		:css('text-align', 'center')
		:wikitext(image)
			:done() --end td
		:done() --end tr
		
end
p.renderAvailableStructures = function(uniprotID_hs, uniprotID_mm, checkOrtholog, pdbIDs)
local title = 'PDBに登録されている構造' --**lclz*    local pdb_link = "PDB" --**lclz*    local searchTitle = "" 
local listTitle = "PDBのIDコード一覧" --**lclz*    local RCSB_base = 'https://www.rcsb.org/search?q='
						..'rcsb_polymer_entity_container_identifiers.reference_sequence_identifiers.database_name:UniProt%20AND%20'
						..'rcsb_polymer_entity_container_identifiers.reference_sequence_identifiers.database_accession:'
local PDBe_base = 'https://www.ebi.ac.uk/pdbe/searchResults.html?display=both&term='
local PDBj_base = 'https://pdbj.org/search/pdb?other_db_select=UniProt&other_db_field='
local url_uniprot = " " 


if checkOrtholog == 1 and uniprotID_mm ~= 'n/a' then
	searchTitle = 'オルソログ検索: '
	url_uniprot = uniprotID_mm..','..uniprotID_hs
else
	searchTitle = 'Human UniProt検索: '
	url_uniprot = uniprotID_hs
end
local PDBe_list = " " --create a list with " or " if there is more than one uniprot
local PDBj_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
		PDBj_list = string.gsub(url_uniprot, ",", "+%%7C+") --add |'s inststead of commas
	else
		PDBe_list = url_uniprot
		PDBj_list = url_uniprot
	end

local RCSB = ""..RCSB_base..url_uniprot.." RCSB "
local PDBe = ""..PDBe_base..PDBe_list.." PDBe "
local PDBj = ""..PDBj_base..PDBj_list.." PDBj "

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(RCSB)
						:wikitext(PDBe)
						:wikitext(PDBj)
						: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', 'mw-collapsible mw-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 ""
	end
end
p.renderIdentifiers = function(aliases, hgnc_id, gene_symbol, homologene_id, omim_id, mgi_id, ChEMBL_id, IUPHAR_id, ec_no, entrez_gene)
	local title = "識別子" --**lclz*	local label_aliases = " 記号" --**lclz*	local symbol_url 
	if gene_symbol == "" or gene_symbol == nil  then
		symbol_url = ""
	else
		if hgnc_id == "" or hgnc_id == nil  then
			symbol_url = gene_symbol
			
		else
			symbol_url = " "..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 end
	local label_ext_id = "外部ID" --**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 ~= "") then
		omim = "OMIM:".." " --**lclz*	end
	for i, v in ipairs(omim_list) do
		if string.match(v, '%w+') then
			omim = omim.." "..v..", "
		end
	end
	omim = string.gsub(omim, ", $"," ")	--remove comma from end
	
	homologene_id = string.gsub(homologene_id, "%s", "")
	local homolo_list = mw.text.split(homologene_id, "、")
	local homolo =""
	if (homologene_id ~= nil and homologene_id ~= "") then
		homolo = "HomoloGene:".." "
	end
	for i, v in ipairs(homolo_list) do
		if string.match(v, '%w+') then
			homolo = homolo.." "..v.." "
		end
	end
	homolo = string.gsub(homolo, ", $"," ")	--remove comma from end
	
	local genecards = "GeneCards:".." "
	genecards = genecards.." "..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 ~= "") then
		mgi = "MGI:".." " --**lclz*	end
	for i, v in ipairs(mgi_list) do
		if string.match(v, '%w+') then
			local mgi_number = string.sub(mgi_id, 5)
			mgi = mgi.." "..mgi_number.." "
		end
	end
	mgi = string.gsub(mgi, ", $"," ")--remove comma from end
	local ChEMBL = ""
	if string.match(ChEMBL_id, '%w+') then
		ChEMBL = "ChEMBL:".." ".." "..ChEMBL_id.." "
	end
	local IUPHAR = ""
	if string.match(IUPHAR_id, '%w+') then 
		IUPHAR = "IUPHAR:".." ".." "..IUPHAR_id.." " --**lclz*	end -- *lclz	local label_EC = "EC番号" --**lclz*	ec_no = string.gsub(ec_no, "%d%.%d+%.%d+%.%-,", "")--remove those with"-" in list
	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 = " .. 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 tr
	if 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
end
end
p.renderDiseases = function(frame, disease, dis_ref, name, qid) 
	local title = "遺伝的関連疾患" --**lclz*
	--check first to see if any of the diseases have references
	local ref_flag_all = false --check if any disease have references if not then don't render the headers
	local disease_name =  --local disease_name = table.concat(disease, ", ")
	for index,value in ipairs(disease) do
		if (dis_refindex ~= nil and dis_refindex ~= ) then
			if disease_name ==  then
				disease_name = value
			else
				disease_name = disease_name..", "..value -- *lclz*: punctuation
			end
			ref_flag_all = true
		end		
	end
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 disease
		local title = ""..name.."と遺伝的に関連している疾患をウィキデータで閲覧・編集"
		local ref_link = disease_name..frame:extensionTag("ref",frame:expandTemplate{ title = 'citation2', 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 = "有効薬剤" --**lzlc*
--check first to see if any of the drugs have references
	local ref_flag_all = false --check if any drugs have references if not then don't render the headers
	drug_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 
		
	--end
	for index,value in ipairs(drug) do
		if (drug_refindex ~= nil and drug_refindex ~= ) then
			protein_qid = drug_pqidindex
			if drug_list_per_proteinprotein_qid ==  or drug_list_per_proteinprotein_qid == nil then
				drug_list_per_proteinprotein_qid = value
			else
				-- *lclz*: comma
			    drug_list_per_proteinprotein_qid = drug_list_per_proteinprotein_qid..', '..value --each list of drugs keyed on protein qid 
			end
			ref_flag_all = true
		end		
	end
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 = ""..drug_pnamek.."と物理的に相互作用する薬剤についてウィキデータで閲覧・編集"
	    	local ref_link = drug_name..frame:extensionTag("ref",frame:expandTemplate{ title = 'citation2', 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

end
p.renderGeneLocation = function(frame, chr, gstart, gend, db, ensembl, chr_mm, gstart_mm, gend_mm, db_mm, ensembl_mm, name)
		local titleHuman = "遺伝子の位置 (ヒト)" --**lclz*		local titleMouse = "遺伝子の位置 (マウス)" --**lclz*        local label_chr = "染色体" --**lclz*        local label_locus = "バンド" --**lclz*        local label_gstart = "開始点" --**lclz*        local label_gend = "終点" --**lclz*        local tooltip_arrowSign = name.."遺伝子の位置" --**lclz*        local arrowSign_width = 14
				
	if 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" = 248956422
				chrLengthTable"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" = 57227415
				chrLengthTable"MT" = 16569
		local chrLength = chrLengthTablechr
		
		--Different languages have different word order.
		local chrTextTable = {}--**lclz*				chrTextTable"1" = "1番染色体 (ヒト)"
				chrTextTable"2" = "2番染色体 (ヒト)"
				chrTextTable"3" = "3番染色体 (ヒト)"
				chrTextTable"4" = "4番染色体 (ヒト)"
				chrTextTable"5" = "5番染色体 (ヒト)"
				chrTextTable"6" = "6番染色体 (ヒト)"
				chrTextTable"7" = "7番染色体 (ヒト)"
				chrTextTable"8" = "8番染色体 (ヒト)"
				chrTextTable"9" = "9番染色体 (ヒト)"
				chrTextTable"10" = "10番染色体 (ヒト)"
				chrTextTable"11" = "11番染色体 (ヒト)"
				chrTextTable"12" = "12番染色体 (ヒト)"
				chrTextTable"13" = "13番染色体 (ヒト)"
				chrTextTable"14" = "14番染色体 (ヒト)"
				chrTextTable"15" = "15番染色体 (ヒト)"
				chrTextTable"16" = "16番染色体 (ヒト)"
				chrTextTable"17" = "17番染色体 (ヒト)"
				chrTextTable"18" = "18番染色体 (ヒト)"
				chrTextTable"19" = "19番染色体 (ヒト)"
				chrTextTable"20" = "20番染色体 (ヒト)"
				chrTextTable"21" = "21番染色体 (ヒト)"
				chrTextTable"22" = "22番染色体 (ヒト)"
				chrTextTable"X" = "X染色体"
				chrTextTable"Y" = "Y染色体"
				chrTextTable"MT" = "ミトコンドリアDNA (ヒト)"
		local chrText = chrTextTablechr
		
		--about the calculation below, see https://en.wikipedia.org/wiki/User:Was_a_bee/Gene#3._Calculation_detail
		local markerWidth = ((gend - gstart) * 294.133 )/ chrLength
		if markerWidth "
			--wikitext_for_ideogram_image  = wikitext_for_ideogram_image..""
			--wikitext_for_ideogram_image  = wikitext_for_ideogram_image..""..chrText..""
			--wikitext_for_ideogram_image  = wikitext_for_ideogram_image..""
			--wikitext_for_ideogram_image  = wikitext_for_ideogram_image..""
		
		else -- wikitext for autosome and sex chromosome
			wikitext_for_ideogram_image = wikitext_for_ideogram_image..""
			wikitext_for_ideogram_image = wikitext_for_ideogram_image..""
			wikitext_for_ideogram_image = wikitext_for_ideogram_image..""..chrText..""
			wikitext_for_ideogram_image = wikitext_for_ideogram_image..""
			wikitext_for_ideogram_image = wikitext_for_ideogram_image..""..tooltip_arrowSign..""
			wikitext_for_ideogram_image = wikitext_for_ideogram_image..""..tooltip_arrowSign..""
			wikitext_for_ideogram_image = wikitext_for_ideogram_image..""
			wikitext_for_ideogram_image = wikitext_for_ideogram_image..""
	end
		
	root
		:tag('tr')
	:tag('td')
				:attr('colspan', 4)
	:css('text-align', 'center')
	:css('background-color', rowBGcolor)
	:tag('table')
		:attr('class', 'mw-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', 'white !important')
							:wikitext(""..chrText.."")
							:done() --end td
						:done() --end tr
					:tag('tr')
						:tag('th')
							:attr('scope', 'row')
							:css('background-color', sideTitleBGcolor)
							:wikitext(label_chr)
							:done() --end th
						:tag('td')
							:attr('colspan', '3')
							: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')
							:css('background-color', sideTitleBGcolor)
							:wikitext(label_locus)
							:done() --end th
						:tag('td')
							:attr('rowspan', '2')
							:css('background-color', rowBGcolor)
							:tag('span')
								:attr('class', 'plainlinks')
								:wikitext("データ無し")
								: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).." 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).." bp"..source_link_gend)
								:done() --end span
							 :done() --end td
						:done() --end tr
					:done() --end table
				 :done() --end td
			:done() --end tr
	end
	
	if 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.p5
		local chrLengthTable_mm = {}
				chrLengthTable_mm"1" = 195471971
				chrLengthTable_mm"2" = 182113224
				chrLengthTable_mm"3" = 160039680
				chrLengthTable_mm"4" = 156508116
				chrLengthTable_mm"5" = 151834684
				chrLengthTable_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" = 120129022
				chrLengthTable_mm"13" = 120421639 
				chrLengthTable_mm"14" = 124902244
				chrLengthTable_mm"15" = 104043685
				chrLengthTable_mm"16" = 98207768
				chrLengthTable_mm"17" = 94987271 
				chrLengthTable_mm"18" = 90702639 
				chrLengthTable_mm"19" = 61431566 
				chrLengthTable_mm"X" = 171031299
				chrLengthTable_mm"Y" = 91744698
				chrLengthTable_mm"MT" = 16299
		local chrLength_mm = chrLengthTable_mmchr_mm
			
		--Different languages have different word order.
		local chrTextTable_mm = {}--**lclz*				chrTextTable_mm"1" = "1番染色体 (マウス)"
				chrTextTable_mm"2" = "2番染色体 (マウス)"
				chrTextTable_mm"3" = "3番染色体 (マウス)"
				chrTextTable_mm"4" = "4番染色体 (マウス)"
				chrTextTable_mm"5" = "5番染色体 (マウス)"
				chrTextTable_mm"6" = "6番染色体 (マウス)"
				chrTextTable_mm"7" = "7番染色体 (マウス)"
				chrTextTable_mm"8" = "8番染色体 (マウス)"
				chrTextTable_mm"9" = "9番染色体 (マウス)"
				chrTextTable_mm"10" = "10番染色体 (マウス)"
				chrTextTable_mm"11" = "11番染色体 (マウス)"
				chrTextTable_mm"12" = "12番染色体 (マウス)"
				chrTextTable_mm"13" = "13番染色体 (マウス)"
				chrTextTable_mm"14" = "14番染色体 (マウス)"
				chrTextTable_mm"15" = "15番染色体 (マウス)"
				chrTextTable_mm"16" = "16番染色体 (マウス)"
				chrTextTable_mm"17" = "17番染色体 (マウス)"
				chrTextTable_mm"18" = "18番染色体 (マウス)"
				chrTextTable_mm"19" = "19番染色体 (マウス)" 
				chrTextTable_mm"X" = "X染色体 (マウス)"
				chrTextTable_mm"Y" = "Y染色体 (マウス)" 
				chrTextTable_mm"MT" = "ミトコンドリアDNA (マウス)" 
		local chrText_mm = chrTextTable_mmchr_mm
		
		--about the calculation below, see https://en.wikipedia.org/wiki/User:Was_a_bee/Gene#3._Calculation_detail
		local markerWidth_mm = ((gend_mm - gstart_mm) * 294.133 )/ chrLength_mm
		if markerWidth_mm "
			--wikitext_for_ideogram_image_mm = wikitext_for_ideogram_image_mm..""
			--wikitext_for_ideogram_image_mm = wikitext_for_ideogram_image_mm..""..chrText_mm..""
			--wikitext_for_ideogram_image_mm = wikitext_for_ideogram_image_mm..""
			--wikitext_for_ideogram_image_mm = wikitext_for_ideogram_image_mm..""
		
		else -- wikitext for autosome and sex chromosome
			wikitext_for_ideogram_image_mm = wikitext_for_ideogram_image_mm..""
			wikitext_for_ideogram_image_mm = wikitext_for_ideogram_image_mm..""
			wikitext_for_ideogram_image_mm = wikitext_for_ideogram_image_mm..""..chrText_mm..""
			wikitext_for_ideogram_image_mm = wikitext_for_ideogram_image_mm..""
			wikitext_for_ideogram_image_mm = wikitext_for_ideogram_image_mm..""..tooltip_arrowSign..""
			wikitext_for_ideogram_image_mm = wikitext_for_ideogram_image_mm..""..tooltip_arrowSign..""
			wikitext_for_ideogram_image_mm = wikitext_for_ideogram_image_mm..""
			wikitext_for_ideogram_image_mm = wikitext_for_ideogram_image_mm..""
		end
		
	root	
		:tag('tr')
	:tag('td')
				:attr('colspan', 4)
	:css('text-align', 'center')
	:css('background-color', rowBGcolor)
	:tag('table')
		:attr('class', 'mw-collapsible mw-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', 'white !important')
							:wikitext(""..chrText_mm.."")
							:done() --end td
						:done() --end tr
					:tag('tr')
						:tag('th')
							:attr('scope', 'row')
							:css('background-color', sideTitleBGcolor)
							:wikitext(label_chr)
							:done() --end th
						:tag('td')
							:attr('colspan', '3')
							: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')
							:css('background-color', sideTitleBGcolor)
							:wikitext(label_locus)
							:done() --end th
						:tag('td')
							:attr('rowspan', '2')
							:css('background-color', rowBGcolor)
							:tag('span')
								:attr('class', 'plainlinks')
								:wikitext("データ無し")
								: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).." 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).." bp"..source_link_gend_mm)
								:done() --end span
							 :done() --end td
						:done() --end tr
					:done() --end table
				 :done() --end td
			:done() --end tr
	end
end
p.renderRNAexpression = function(expression_images, entrez_gene)
	local title = "RNA発現パターン" --**lclz*	local biogps_link = " さらなる参照発現データ" --**lclz*	root
		:tag('tr')
	:tag('td')
				:attr('colspan', 4)
	:css('text-align', 'center')
	:css('background-color', rowBGcolor)
	:tag('table')
		:attr('class', 'mw-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 tr
end
p.renderGeneOntology = function(mol_funct, cell_comp, bio_process, uniprotID)
	local title = "遺伝子オントロジー" --**lclz*	local mol_funct_title = "分子機能" --**lclz*	local cell_comp_title = "細胞の構成要素" --**lclz*	local bio_process_title = "生物学的プロセス" --**lclz*	local amigo_link = " .. " Amigo"
	local quickGO_link = " .. " QuickGO"
	root
		:tag('tr')
	:tag('td')
				:attr('colspan', 4)
	:css('text-align', 'center')
	:css('background-color', rowBGcolor)
	:tag('table')
		:attr('class', 'mw-collapsible mw-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("出典:")
				:wikitext(amigo_link)
				:wikitext(" / ")
				:wikitext(quickGO_link)
				:done() --end td
					:done() --end tr
					:done() --end table
				:done() --end td
			:done() --end tr
end 
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 = "オルソログ" --**lclz*	--to do make the list creation a function
	--create list for entrez ids
	
	-- *lclz*: Category name
	local category_chromosome = 
	if mw.title.getCurrentTitle().namespace ~= 0 then
		category_chromosome = ""
	end
	local entrezTitle = "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" then
			entrez_link_list#entrez_link_list+1 = " "..entrez_gene..""
		end
	end
	--if less than 5 don't create collapsible list
	if  table.getn(entrez_link_list) ' .. table.remove(entrez_link_list, 1) ..  ..table.remove(entrez_link_list, 1) ..  .. table.remove(entrez_link_list, 1) ..  .. table.remove(entrez_link_list, 1) .. --get first 5 elements in table and use for display
	end
	if entrez_link_list#entrez_link_list then
		entrez_link = table.concat(entrez_link_list, "")
	end
	
	--create list for mouse Entrez id
	entrez_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" then
			entrez_mm_link_list#entrez_mm_link_list+1 = " "..v..""
		end
	end
	--if less than 5 don't create collapsible list
	if  table.getn(entrez_mm_link_list) ' .. table.remove(entrez_mm_link_list, 1) ..  ..table.remove(entrez_mm_link_list, 1) ..  .. table.remove(entrez_mm_link_list, 1) ..  .. table.remove(entrez_mm_link_list, 1) .. --get first 5 elements in table and use for display
	end
	if entrez_mm_link_list#entrez_mm_link_list then
		entrez_mm_link = table.concat(entrez_mm_link_list, "")
	end
	
	--create list of ensembl id
	local ensemblTitle = "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" then
			ensembl_link_list#ensembl_link_list+1 = " "..v..""
		end
	end
	--if less than 5 don't create collapsible list
	if  table.getn(ensembl_link_list) ' .. table.remove(ensembl_link_list, 1) ..  ..table.remove(ensembl_link_list, 1) ..  .. table.remove(ensembl_link_list, 1) ..  .. table.remove(ensembl_link_list, 1) .. --get first 5 elements in table and use for display
	end
	if ensembl_link_list#ensembl_link_list then
		ensembl_link = table.concat(ensembl_link_list, "")
	end
	
	--create list of mouse ensembl id
	local ensemblTitle = "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" then
			ensembl_mm_link_list#ensembl_mm_link_list+1 = " "..v..""
		end
	end
	--if less than 5 don't create collapsible list
	if  table.getn(ensembl_mm_link_list) ' .. table.remove(ensembl_mm_link_list, 1) ..  ..table.remove(ensembl_mm_link_list, 1) ..  .. table.remove(ensembl_mm_link_list, 1) ..  .. table.remove(ensembl_mm_link_list, 1) .. --get first 5 elements in table and use for display
	end
	if ensembl_mm_link_list#ensembl_mm_link_list then
		ensembl_mm_link = table.concat(ensembl_mm_link_list, "")
	end
	--create lists of uniprot ID
	local uniprotTitle = "UniProt"
	local uniprot_url = "http://www.uniprot.org/uniprot/"
	
	local uniprot_link = "n/a"
	local uniprot_collapse
	local uniprot_default = ""
	--split string and loop through concatenate by 
	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 exist
	local uniprot_alternate = {} --A-N,R-Z entries
	local hash = {} --storage to look for duplicated values 
	for k,v in ipairs(split_uniprot) do 
		if not hashv 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_first#uniprot_first+1 = "" .. concat_uniprot_link .. " " ..label .. ""
				else
					uniprot_alternate#uniprot_alternate+1 = "" .. concat_uniprot_link .. " " ..label .. ""
				end
			end
			hashv = true
		end
	end
if table.getn(uniprot_first)>0 then --if there is something in the preferred values display else display anything else
		uniprot_link_list  = uniprot_first
	else
		uniprot_link_list  = uniprot_alternate
	end
	
	--if less than 5 don't create collapsible list
	if  table.getn(uniprot_link_list) ' .. table.remove(uniprot_link_list, 1) ..  ..table.remove(uniprot_link_list, 1) ..  .. table.remove(uniprot_link_list, 1) ..  .. table.remove(uniprot_link_list, 1) .. --get first 5 elements in table and use for display
	end
	
	if uniprot_link_list#uniprot_link_list then
		uniprot_link = table.concat(uniprot_link_list, "")
	end
	
--mouse uniprot lists
	local uniprot_mm_link = "n/a"
	local uniprot_mm_collapse
	local uniprot_mm_default = ""
	--split string and loop through concatenate by 
	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 values
	for k,v in ipairs(split_uniprot_mm) do 
	    if not hashv 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 .. ""
				else
					uniprot_mm_alternate#uniprot_mm_alternate+1 = "" .. concat_uniprot_link .. " " ..label .. ""
				end
		    end
			hashv = true
		end
	end
	if table.getn(uniprot_mm_first)>0 then --if there is something in the preferred values display else display anything else
		uniprot_mm_link_list  = uniprot_mm_first
	else
		uniprot_mm_link_list  = uniprot_mm_alternate
	end
	--if less than 5 don't create collapsible list
	if  table.getn(uniprot_mm_link_list) ' .. table.remove(uniprot_mm_link_list, 1) ..  ..table.remove(uniprot_mm_link_list, 1) ..  .. table.remove(uniprot_mm_link_list, 1) ..  .. table.remove(uniprot_mm_link_list, 1) .. --get first 5 elements in table and use for display
	end
	
	if uniprot_mm_link_list#uniprot_mm_link_list then
		uniprot_mm_link = table.concat(uniprot_mm_link_list, "")
	end
	
	local 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 mRNA
	local refseq_mRNA_link = "n/a"
	local refseq_mRNA_collapse
	local refseq_mRNA_default = ""
	--split string and loop through concatenate by 
	local split_refseq_mRNA = mw.text.split(refseq_mRNA, "、")
	local link_list_first = {} --hold those the have NM or NP values
	local link_list_alternate = {} --hold those that are XM or XP values
	local link_list = {} --if NM,NP display if not display XM, XP values 
	for k,v in ipairs(split_refseq_mRNA) do
		local label = mw.text.trim(v)
		local concat_ncbi_link = ncbi_link .. label
		if string.match(v, '%w+') and v ~= "n/a" then
			if 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') then
				link_list_alternate#link_list_alternate+1 = "" .. concat_ncbi_link .. " " ..label .. ""
			end
		end
end
	if table.getn(link_list_first)>0 then
		link_list = link_list_first
	else
		link_list = link_list_alternate
	end
	
	--if less than 5 don't create collapsible list
	if  table.getn(link_list) ' .. table.remove(link_list, 1) ..  ..table.remove(link_list, 1) ..  .. table.remove(link_list, 1) ..  .. table.remove(link_list, 1) .. --get first 5 elements in table and use for display
	end
	
	if link_list#link_list then
		refseq_mRNA_link = table.concat(link_list, "")
	end
	
	
	--create list of links for refSeq mRNA for mouse
	local refseq_mRNA_mm_link = "n/a"
	local refseq_mRNA_mm_collapse
	local 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 values
	local link_list_first = {} --hold those the have NM or NP values
	local link_list_alternate = {} --hold those that are XM or XP values

	for k,v in ipairs(split_refseq_mRNA_mm) do
		local label = mw.text.trim(v)
		local concat_ncbi_link = ncbi_link .. label
		if string.match(v, '%w+') and v ~= "n/a" then
			if 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') then
				link_list_alternate#link_list_alternate+1 = "" .. concat_ncbi_link .. " " ..label .. ""
			end
		end
end
	if table.getn(link_list_first)>0 then
		link_list_mm = link_list_first
	else
		link_list_mm = link_list_alternate
	end
	--if less than 5 don't create collapsible list
	if  table.getn(link_list_mm) ' .. table.remove(link_list_mm, 1) ..  ..table.remove(link_list_mm, 1) ..  .. table.remove(link_list_mm, 1) ..  .. table.remove(link_list_mm, 1) .. --get first 5 elements in table and use for display
	end
	if link_list_mm#link_list_mm then
		refseq_mRNA_mm_link = table.concat(link_list_mm, "")
	end
	
-- *lclz*: sometimes
	local refseq_protTitle = "RefSeq(タンパク質)"
	--create list of links for human refseq protein
	local 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 values
	local link_list_alternate = {} --hold those that are XM or XP values
	for k,v in ipairs(split_refseq_prot) do
		local label = mw.text.trim(v)
		local concat_ncbi_link = ncbi_link .. label
		if string.match(v, '%w+') and v ~= "n/a" then
			if 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') then
				link_list_alternate#link_list_alternate+1 = "" .. concat_ncbi_link .. " " ..label .. ""
			end
		end
	end
	if table.getn(link_list_first)>0 then
		link_list_prot  = link_list_first
	else
		link_list_prot  = link_list_alternate
	end
	--if less than 5 don't create collapsible list
	if  table.getn(link_list_prot) ' .. table.remove(link_list_prot, 1) ..  ..table.remove(link_list_prot, 1) ..  .. table.remove(link_list_prot, 1) ..  .. table.remove(link_list_prot, 1) .. --get first 5 elements in table and use for display
	end

	if link_list_prot#link_list_prot then
		refseq_prot_link = table.concat(link_list_prot, "")
	end
	
	
	--create list of links for mouse refseq protein
	local refseq_prot_mm_link = "n/a"
	local refseq_prot_mm_collapse
	local 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 values
	local link_list_alternate = {} --hold those that are XM or XP values

	for k,v in ipairs(split_refseq_prot_mm) do
		local label = mw.text.trim(v)
		local concat_ncbi_link = ncbi_link .. label
		if string.match(v, '%w+') and v ~= "n/a" then
			if 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') then
				link_list_alternate#link_list_alternate+1 = "" .. concat_ncbi_link .. " " ..label .. ""
			end
		end
	end
	if table.getn(link_list_first)>0 then
		link_list_prot_mm  = link_list_first
	else
		link_list_prot_mm  = link_list_alternate
	end
	--if less than 5 don't create collapsible list
	if  table.getn(link_list_prot_mm) ' .. table.remove(link_list_prot_mm, 1) ..  ..table.remove(link_list_prot_mm, 1) ..  .. table.remove(link_list_prot_mm, 1) ..  .. table.remove(link_list_prot_mm, 1) .. --get first 5 elements in table and use for display
	end
	if link_list_prot_mm#link_list_prot_mm then
		refseq_prot_mm_link = table.concat(link_list_prot_mm, "")
	end
	
	local locTitle = "場所(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+') )then
		local chr_ucsc 
		if chr == "MT" then  
			chr_ucsc = "M" --UCSC uses "M" (not "MT") in URL for mitochondrial DNA
		else
			chr_ucsc = chr
		end	
		chr_loc_link = " ".."Chr "..chr_ucsc..": "..gstart_mb.." – "..gend_mb.." Mb" 
	else
		chr_loc_link = "n/a"	
	end
	local 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+') )then
		local chr_mm_ucsc 
		if chr_mm == "MT" then  
			chr_mm_ucsc = "M" --UCSC uses "M" (not "MT") in URL for mitochondrial DNA
		else
			chr_mm_ucsc = chr
		end
		chr_loc_mm_link =  " ".."Chr "..chr_mm_ucsc..": "..gstart_mm_mb.." – "..gend_mm_mb.." Mb"
	else
		chr_loc_mm_link = "n/a"	
	end
	local pubmedTitle = "PubMed検索" -- *lclz	local pubmed_link = entrez_gene
	if string.match(entrez_gene, '%w+') and entrez_gene ~= "n/a" then
		pubmed_link = frame:extensionTag("ref",frame:expandTemplate{ title = 'citation2', 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 } } )--expandTemplate creates cite web template url=ref_link..ect 
	end
	local pubmed_mm_link = entrez_gene_mm
	if string.match(entrez_gene_mm, '%w+') and entrez_gene_mm ~= "n/a" then
		pubmed_mm_link = frame:extensionTag("ref",frame:expandTemplate{ title = 'citation2', 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 } } )--expandTemplate creates cite web template url=ref_link..ect
	end
	
	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)
		:wikitext("種") --**lclz*        		:done() --end th
	:tag('td')
		:wikitext("ヒト") --**lclz*        		:done() --end td
	:tag('td')
		:wikitext("マウス") --**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 tr
end
p.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 tr
end
p.renderFooter = function(Qid, Qid_mm)
local text = "ウィキデータ" --**lclz* local hs_link = "閲覧/編集 ヒト" --**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 = "閲覧/編集 マウス" --**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 tr
	root:done() --end root table
end
--this code isn't used was hoping could do some generalization of rows
p.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 object
p.getLabel = function(entity)
	local data = entity
	local f = {'labels','en','value'}
	local i = 1
	while true do
		local index = fi
		if not index then
			if type(data) == "table" then
				return mw.text.jsonEncode(data, mw.text.JSON_PRESERVE_KEYS + mw.text.JSON_PRETTY)
			else
				return tostring(data)
			end
		end
		
		data = dataindex or datatonumber(index)
		if not data then
			return
		end
		
		i = i + 1
	end
end
--general function to get value given an entity and property
p.getValue = function(entity, propertyID, return_val)
	local claims
	if return_val == nil then return_val = "" end
local sep = " " --could ad as input parameter if need be
	if entity and entity.claims then
		claims = entity.claimspropertyID
	end
	if claims then
		-- if wiki-linked value output as link if possible
		if (claims1 and claims1.mainsnak.snaktype == "value" and claims1.mainsnak.datavalue.type == "wikibase-entityid") then
			local out = {}
			for k, v in pairs(claims) do
				local datav = mw.wikibase.label("Q" .. v.mainsnak.datavalue.value"numeric-id")
				if datav == nil then datav = " " end 
				out#out + 1 = datav			
			end
			return table.concat(out, sep)
		else
		-- just return best values
			return entity:formatPropertyValues(propertyID).value
		end
	else
		return return_val
	end
end
p.getValueProtein = function(protein_entities, propertyID, return_val)
	if return_val == nil then return_val = "" end
	local sep = ","
local overall_results = {} --should return empty if nothing assigned
	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 whole
		local claims
		local entity = val --each protein in encodes
		if entity and entity.claims then
			claims = entity.claimspropertyID
		end
		if claims then
			local results
			-- if wiki-linked value output as link if possible
			if (claims1 and claims1.mainsnak.snaktype == "value" and claims1.mainsnak.datavalue.type == "wikibase-entityid") then
				local out = {}
				for k, v in pairs(claims) do
					local datav = mw.wikibase.label("Q" .. v.mainsnak.datavalue.value"numeric-id")
					if datav == nil then datav = " " end 
					out#out + 1 = datav			
				end
				results = table.concat(out, sep)
			else
				results = entity:formatPropertyValues(propertyID).value
			end
			overall_results#overall_results+1 = results --individual propertyID value stored in this index	
		end
	end
	local str_overall_results = table.concat(overall_results, sep) --weirdness happens when add a sep = " " otherwise each value represented one time
	if string.match(str_overall_results, '%w+') then
		return str_overall_results 
	else
		return return_val
	end
end
--general function to get value given an entity and property
p.getQid = function(entity)
	local Qid
	if entity and entity.id then
		Qid = entity.id
		return Qid
	else
		return ""
	end
end
--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 = "" end
	local input_rank = "RANK_PREFERRED" ---this is mostly like won't do anything because ranking isn't maintained in wikidata 
	local claims
	
	if entity.claims then
		claims = entity.claimspropertyID
	end
	if claims then
		-- if wiki-linked value output as link if possible
		if (claims1 and claims1.mainsnak.snaktype == "value" and claims1.mainsnak.datavalue.type == "wikibase-entityid" ) then
			local out = {}
			for k, v in pairs(claims) do
				local 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" end
							
				if sitelink then
					out#out + 1 = "" .. label .. ""
				else
					out#out + 1 = ":d:Q" .. v.mainsnak.datavalue.value"numeric-id" .. "|" .. label .. ""
				end
			end
			return table.concat(out, ", ")
		else
			local 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_split1 then
				preferred_result = mw.text.trim(results_split1) --return first element if desired prefix not found and remove whitespace
			end
			local id --refseq id in question
			for i, id in ipairs(results_split) do
				local 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
				end
			end
			if preferred_result then
				return preferred_result --return a id starting with NP or NM
			else
				return return_val --return first element because desired prefix not found and remove whitespaces
			end
			--
			return results
		end
	else
		return return_val
	end
end
-- *lclz*: same as getRefseq_mRNA
p.getRefseq_protein = function(protein_entities, propertyID, return_val)
local sep = "、"
local overall_results = {} --should return empty if nothing assigned
	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 whole
	
		local claims
		local entity = val --each protein in encodes
		if entity.claims then
			claims = entity.claims"P637"
		end
		if claims then
			local results
			-- if wiki-linked value output as link if possible
			if (claims1 and claims1.mainsnak.snaktype == "value" and claims1.mainsnak.datavalue.type == "wikibase-entityid" ) then
				local out = {}
				for k, v in pairs(claims) do
					local datav = mw.wikibase.label("Q" .. v.mainsnak.datavalue.value"numeric-id")
					if datav == nil then datav = " " end 
					out#out + 1 = datav			
				end
				results = table.concat(out, sep)
			else
				results = entity:formatPropertyValues("P637", mw.wikibase.entity.claimRanks).value 
			end
			overall_results#overall_results+1 = results --a list is in each index 
		end	
		
	end
	--why are there duplicate results here
	local str_overall_results = table.concat(overall_results, sep)
	return str_overall_results
end
	--
	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 element
	
	local preffered_result = results_split1 or ""
	for i, id in ipairs(results_split) do
		local trim_id = mw.text.trim(id)
		--check of id starts with NP or NM
		if string.match( trim_id, '^NP_%d+') then 
			preferred_result = trim_id --overwrite each time found only need one to display
		end
	end
	--check if something in preffered_result if not get first element in result_split
	if p.isempty(preffered_result) then
		return return_val
	else
		return preferred_result --return a id starting with NP or NM
	end
end --
--gets an image
p.getImage = function(entity, propertyID, sep, imgsize)

	local claims

	if entity and entity.claims then  
		claims = entity.claimspropertyID  
	end

	if claims then
		if (claims1 and claims1.mainsnak.datatype == "commonsMedia") then  
			local out = {}  
			for k, v in pairs(claims) do  
				local filename = v.mainsnak.datavalue.value  
				out#out + 1 = "" .. imgsize .. "" 
			end   
				return table.concat(out, sep)   
		else   
			return ""   
		end   
	else   
		return ""   
	end   
end
p.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 whole
		local claims
		local entity = val
		if entity and entity.claims then
			claims = entity.claimspdb_propertyID
		end
		local sitelink = "https://www.wwpdb.org/pdb?id=pdb_0000"
		if claims then
			local results
			if (claims1 and claims1.mainsnak.snaktype == "value") then
			
			
				local out = {}
				for k, v in pairs(claims) do
					local label = mw.wikibase.label(v.mainsnak.datavalue.value)
					if label == nil then label = v.mainsnak.datavalue.value end
				
					if sitelink then
						out#out + 1 = "" .. sitelink .. label .. " " ..label .. ""
					else
						out#out + 1 = "" .. label .. ""
					end
				end
				results = table.concat(out, ", ") -- *lclz*: punctuation (CJK comma, etc.)
			else
				results = entity:formatPropertyValues(propertyID, mw.wikibase.entity.claimRanks).value
			end
			overall_results#overall_results+1 = results --individual propertyID values stored in this index
		end
	end
	return table.concat(overall_results, ",%%s")
end
function 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'aliasesen'
if test then
			for key, value in ipairs(test) do
				a = a .. ', ' ..  value'value'
			end
			return a
		else
			return ""
		end
	else
		return ""
	end
	
end
--get a geneome start P644 or end P645
p.getChromosomeLoc = function(entity, propertyID, prefix)
	-- will contain the numeric value for the requested coordinate
	local 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.args1 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 function
	local qualifierID = "P659" --mw.text.trim(frame.args2 or "")
	-- Why do we include this here?  What should happen if FETCH_WIKIDATA is not included? 
	--local input_parm = mw.text.trim(frame.args3 or "")
	-- this can needs to be fed to the function either by a call to 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.args4 or "")
	-- will track the different builds pulled from the qualifiers
	local 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 Q19847637
	if entity and entity.claims then
		claims = entity.claimspropertyID
	end
	--will return nothing if no claims are found
	if claims then
		--checking to be sure claims is populated, not sure it its needed
		if (claims1 ) then
			--useful for debugging
			--local out = {}
			--pulls the genome location from the claim
			for k, v in pairs(claims) do
				local location = v.mainsnak.datavalue.value
				--debugging
				--out#out + 1 = k.." location:" .. location.. " 
" 
				--gets the qualifiers linked to the current claim
				local quals 
				if v.qualifiers then
					quals = v.qualifiers.P659
				end
				--if there are any
				if quals then
					for qk, qv in pairs(quals) do
						local qual_obj_id = "Q"..qv.datavalue.value"numeric-id"
						--get to the entity targeted by the qualifier property.  Genome builds are Items in wikidata
						local 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 bot
						if qual_obj"aliases" ~= nil then
							local test = qual_obj"aliases""en"
							for key, value in ipairs(test) do
								if string.match(value'value', prefix) then
									alias = 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 then
										output = location
										newest_build = build_no
									end
								end
							end
						end
					end
				--in case there are no qualifiers, but there is a location, might as well return it
				else output = location 
				end
			end
				return output
		else
			return ""
		end
	else
		return ""
		--debug
		--"no claims for "..itemID.." prop "..propertyID
	end
end
p.getAliasFromGenomeAssembly = function(entity, prefix)
	-- will contain the numeric value for the requested coordinate
	local output = ""
	local sep = " "
	local propertyID = "P644" --genomic start used 
	local qualifierID = "P659" --genomic assembly
	local newest_build = "0"
	local claims
	if entity.claims then
	 claims = entity.claimspropertyID
	end
	--will return nothing if no claims are found
	if claims then
		--checking to be sure claims is populated, not sure it its needed
		if (claims1 ) then
			--useful for debugging
			--local out = {}
			--pulls the genome location from the claim
			for k, v in pairs(claims) do
				local quals
				if v.qualifiers then
					quals = v.qualifiers.P659
				end
				--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 then
					for qk, qv in pairs(quals) do
						local qual_obj_id = "Q"..qv.datavalue.value"numeric-id"
						--get to the entity targeted by the qualifier property.  Genome builds are Items in wikidata
						local 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 bot
						if qual_obj"aliases" ~= nil then
							local test = qual_obj"aliases""en"
							for key, value in ipairs(test) do
								if string.match(value'value', prefix) then
									alias = 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 then
										newest_build = build_no
									end
								end
							end
						end
					end
				--in case there are no qualifiers, but there is a location, might as well return it
				else output = location 
				end
			end
				return prefix..newest_build
		else
			return ""
		end
	else
		return ""
	end
end
-- *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') or string.find(string_to_trim, 'ミトコンドリア') then --match both 'mitochondrio'/'mitochondrial'
		out = "MT"
	elseif string.find(string_to_trim, 'chromosome') or string.find(string_to_trim, '染色体') then
		out = string.match(string_to_trim, "%d+")--extract number from string
		if out == nil then
			out = string.match(string_to_trim, "X") or string.match(string_to_trim, "Y")
		end
	end
	return out	
end
p.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
end
end
p.isempty = function(s)
	return s == nil or s == 
end
p.getGO = function(protein_entities, propertyID)
	--propertyID ie molecular, cellular, function
	
	local overall_results = {}
	local results = "" --string to return
	
	for key, val in pairs(protein_entities) do
	
		local claims
		local entity = val
		if entity.claims then
			claims = entity.claimspropertyID -- ie molecular, cellular, function
		end
		local propertyID_child = "P686" -- Gene Ontology ID
		
		if claims then
			
			if (claims1 and claims1.mainsnak.snaktype == "value" and claims1.mainsnak.datavalue.type == "wikibase-entityid") then
				--local out = {}
				for k, v in pairs(claims) do
					local itemID_child = "Q" .. v.mainsnak.datavalue.value"numeric-id" --get Qid of property item so can get the GOid
					local entity = mw.wikibase.getEntityObject(itemID_child)
					local claims
					local result_GOID = 
					if entity and entity.claims then claims = entity.claimspropertyID_child end
					if claims then
						result_GOID = entity:formatPropertyValues(propertyID_child, mw.wikibase.entity.claimRanks).value
					else
						result_GOID = nil --no GO ID
					end
					local 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" end
					local wiki_link	= ""
					if sitelink and result_GOID ~= nil then
						wiki_link = "• " .. sitelink .. result_GOID .. " " .. label ..""
					else
						wiki_link = "• :d:Q" .. v.mainsnak.datavalue.value"numeric-id" .. "|" .. label .. ""
					end
					overall_results#overall_results+1 = wiki_link
				end
				
			else
				results = entity:formatPropertyValues(propertyID, mw.wikibase.entity.claimRanks).value
			end
			
		end
		--overall_results#overall_results+1 = results --each protein GO terms stored in this index, so table contains all the GO terms with duplicates 
	end
	local hash = {} --temp check
	local res = {} --no dups
	for _,v in ipairs(overall_results) do
		if (not hashv) then
		res#res+1 = v 
		hashv = true
		end
	end
	return table.concat(res, "")
end
local 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
	--end
	local data = entity
	if not data then
		return nil
	end
	

	local i = 1
	while true do
		local index = fi
		if not index then
			if type(data) == "table" then
				return mw.text.jsonEncode(data, mw.text.JSON_PRESERVE_KEYS + mw.text.JSON_PRETTY)
			else
				return tostring(data)
			end
		end
		
		data = dataindex or datatonumber(index)
		if not data then
			return ""
		end
		i = i + 1
	end
end
p.getDisease= function(entity, propertyID)
local claims
	if return_val == nil then return_val = "" end
	if entity and entity.claims then
		claims = entity.claimspropertyID
	end
	if claims then
		-- if wiki-linked value output as link if possible
		
		if (claims1 and claims1.mainsnak.snaktype == "value" and claims1.mainsnak.datavalue.type == "wikibase-entityid") then
			local out = {}
			local datasource = {}
			--value
			--maybe there is a more direct way to find this than looping through the json object
			
			for k, v in pairs(claims) do
				local 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 = ref
				end
		    
--if refLink = "" then --skip if there isn't a reference found
				
				if linkTarget then
					out#out + 1 = ""..datav..""
				else
					out#out + 1 = "" .. datav .. ""
				end
				datasource#out = refLink
				--end				
			end
			return out, datasource
		else
		-- just return best values
			--return entity:formatPropertyValues(propertyID).value
			return return_val, return_val
		end
	else
		return return_val
	end	
return return_val
end
p.getDrug= function(protein_entities, propertyID)
local out = {}
	local datasource = {}
	local pname = {}
	local pqid = {}
	for key, val in pairs(protein_entities) do
		local claims
		local entity = val
		local name = check_values(p.getLabel,{entity})
		if entity.claims then
			claims = entity.claimspropertyID -- ie physically interacts with
		end
		local protein_id
		if entity then protein_id = entity.id else protein_id = "" end
		if claims then
			if (claims1 and claims1.mainsnak.snaktype == "value" and claims1.mainsnak.datavalue.type == "wikibase-entityid") then
				for k, v in pairs(claims) do
					local 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 = getReference(protein_id, entity, "P129",k)  --just check if anything returned
					if (ref ~= nil and ref ~= ) then
				    	refLink = ref
				    end
					if linkTarget then
					    out#out + 1 = ""..datav..""
				    else
					    out#out + 1 = "" .. datav .. ""
				    end
					pnameprotein_id = name
				    pqid#out = protein_id
					datasource#out = refLink
				end --end k,v claims loop
			end --end claims1
		end --if claims
end -- end protein_entities loop
	return out, datasource, pqid, pname
end
p.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 commaSeparated
end
return p