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script.js
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$(document).ready(function () {
$('[data-toggle="tooltip"]').tooltip();
var availableTags = [];
var taxids = {};
var jbrowse_url;
var queryOrgs = [
"SELECT ?species ?speciesLabel ?taxid ?RefSeq",
"WHERE { ?species wdt:P171* wd:Q10876;",
"wdt:P685 ?taxid; wdt:P2249 ?RefSeq.",
"SERVICE wikibase:label {",
"bd:serviceParam wikibase:language \"en\" .}}"].join(" ");
$.ajax({
type: "GET",
url: "https://query.wikidata.org/sparql?format=json&query=" + queryOrgs,
dataType: 'json',
success: function (data) {
$.each(data['results']['bindings'], function (key, element) {
availableTags.push(element['speciesLabel']['value']);
taxids[element['speciesLabel']['value']] = [element['taxid']['value'],
element['species']['value'],
element['RefSeq']['value'],
element['speciesLabel']['value']];
});
}
});
$(function () {
$("#orgform").autocomplete({
source: availableTags
});
});
$("#button1").off("click").click(function (event) {
$("#gene_form_div").html("<form class=\"form-inline ui-widget\"> <div class=\"form-group\"> " +
"<label for=\"geneForm\">Gene/Protein Selection:</label> <input type=\"text\" class=\"form-control formborders\" id=\"geneForm\" " +
"name=\"geneFormItem\" placeholder=\"choose a gene\"> </div> <button id=\"button2\" type=\"submit\" " +
"class=\"btn btn-primary formborders\">Select</button> </form>");
var availablegeneTags = [];
event.preventDefault();
$('div.geneData').empty();
$('div.proteinData').empty();
var organism = $('input[name=orgFormItem]').val();
var current_taxid = taxids[organism];
var orgqid = current_taxid[1].split('/');
$("#orgName").html("<h3><i>" + current_taxid[3] + "</i></h3>");
$("div.orgData").html("<span><div class=\"dataul\"> <h4>NCBI Taxonomy ID:</h4>" + "<a target=\"_blank\" href=https://www.ncbi.nlm.nih.gov/taxonomy/" + current_taxid[0] + ">" + current_taxid[0] + "</a>" + "</div></span>" +
"<span><div class=\"dataul\"> <h4>NCBI RegSeq Accession:</h4>" + "<a target=\"_blank\" href=http://www.ncbi.nlm.nih.gov/nuccore/" + current_taxid[2] + ">" + current_taxid[2] + "</a>" + "</div></span>" +
"<span><div class=\"dataul\"> <h4>Wikidata Item ID:</h4>" + "<a target=\"_blank\" href=" + current_taxid[1] + ">" + orgqid.slice(-1)[0] + "</a>" + "</div></span>"
);
$("#orgbut").html("<button data-toggle=\"tooltip\" title=\"Go to the Wikidata page for the microbe " + current_taxid[3] + "\"" + "id=\"wdorgbut\" class=\"wdbutton btn btn-default\"><img id=\"wdlogo1\" src=\"img/GeneWikidata-logo-en.png\"></button>");
$("#orgform").val("");
$('#wdorgbut').off("click").click(function () {
$(this).html("<a target=\"_blank\" href=" + current_taxid[1] + "> <img id=\"wdlogo1\" src=\"img/GeneWikidata-logo-en.png\"></a>");
});
var defaultCoords = "&tracklist=0&menu=0&loc=" + current_taxid[2] + ":" + "100000..200000&tracks=genes_canvas_mod";
jbrowse_url = "JBrowse-1.12.1-dev/index.html?data=sparql_data/sparql_data_" + current_taxid[0];
$('#jbrowse').html("<span><iframe src=" + jbrowse_url + defaultCoords + "></iframe> </span>");
var tid = current_taxid[0].trim();
var queryGenes = ["SELECT ?gene ?specieswd ?specieswdLabel ?taxid ?genomeaccession ?geneLabel ",
"?locustag ?entrezid ?genomicstart ?genomicend ?strand ?protein ?proteinLabel ?uniprot ?refseqProtein ",
"WHERE {",
"?specieswd wdt:P685",
"\"" + tid + "\".",
"?specieswd wdt:P685 ?taxid;",
"wdt:P2249 ?genomeaccession.",
"?gene wdt:P703 ?specieswd;",
"wdt:P351 ?entrezid ;",
"wdt:P644 ?genomicstart;",
"wdt:P645 ?genomicend;",
"wdt:P2393 ?locustag;",
"wdt:P2548 ?strand.",
"OPTIONAL{?gene wdt:P688 ?protein.",
"?protein wdt:P352 ?uniprot;",
"wdt:P637 ?refseqProtein.}",
"SERVICE wikibase:label {",
"bd:serviceParam wikibase:language \"en\" .",
"}}"
].join(" ");
$.ajax({
type: "GET",
url: "https://query.wikidata.org/sparql?format=json&query=" + queryGenes,
dataType: 'json',
success: function (data) {
$.each(data['results']['bindings'], function (key, element) {
availablegeneTags.push(element['geneLabel']['value']);
});
var genes = data['results']['bindings'];
var i = null;
$(function () {
$("#geneForm").autocomplete({
source: availablegeneTags
});
});
$("#button2").off("click").click(function (event2) {
console.log(taxids[current_taxid[3]]);
event2.preventDefault();
var gene = $('input[name=geneFormItem]').val();
for (i = 0; genes.length > i; i += 1) {
if (genes[i]['geneLabel']['value'] === gene) {
var gstart = genes[i]['genomicstart']['value'] - 400;
var gend = genes[i]['genomicend']['value'] - (-400);
var coords = "&tracklist=0&menu=0&loc=" + genes[i]['genomeaccession']['value'] + ":" + gstart + ".." + gend;
var gene_wd_uri = genes[i]['gene']['value'];
var geneqid = gene_wd_uri.split('/');
//$("#geneName").html("<h3>" + genes[i]['geneLabel']['value'] + "</h3>");
$("div.geneData").html("<span><div class=\"dataul\"> <h4>Gene Name:</h4>" + genes[i]['geneLabel']['value'] + "</div></span>" +
"<span><div class=\"dataul\"> <h4>Locus Tag:</h4>" + "<a target=\"_blank\" href=http://www.ncbi.nlm.nih.gov/gene/?term=" + genes[i]['locustag']['value'] + ">" + genes[i]['locustag']['value'] + "</a>" + "</div></span>" +
"<span><div class=\"dataul\"> <h4>Entrez ID:</h4>" + "<a target=\"_blank\" href=http://www.ncbi.nlm.nih.gov/gene/?term=" + genes[i]['entrezid']['value'] + ">" + genes[i]['entrezid']['value'] + "</a>" + "</div></span>" +
"<span><div class=\"dataul\"> <h4>Genome Start:</h4>" + genes[i]['genomicstart']['value'] + "</div></span>" +
"<span><div class=\"dataul\"> <h4>Genome End:</h4>" + genes[i]['genomicend']['value'] + "</div></span>" +
"<span><div class=\"dataul\"> <h4>Wikidata Item ID:</h4>" + "<a target=\"_blank\" href=" + genes[i]['gene']['value'] + ">" + geneqid.slice(-1)[0] + "</a>" + "</div></span>"
);
$("#genebut").html("<button data-toggle=\"tooltip\" title=\"Go to the Wikidata page for the gene "
+ genes[i]['geneLabel']['value'] + "\"" + "id=\"wdgenebut\" class=\"wdbutton btn btn-default\"><img id=\"wdlogo2\" " +
"src=\"img/GeneWikidata-logo-en.png\"></button>");
console.log(genes[i]['gene']['value']);
$('#wdgenebut').off("click").click(function () {
$(this).html("<a target=\"_blank\" href=" + gene_wd_uri + "> <img id=\"wdlogo2\" src=\"img/GeneWikidata-logo-en.png\"></a>");
});
$('#jbrowse').html("<span><iframe src=" + jbrowse_url + coords + "></iframe> </span>");
var prot_wd_uri = genes[i]['protein']['value'];
var protqid = prot_wd_uri.split('/');
//$("#protName").html("<h3>" + genes[i]['proteinLabel']['value'] + "</h3>");
$("div.proteinData").html("<span><div class=\"dataul\"> <h4>Protein Name:</h4>" + genes[i]['proteinLabel']['value'] + "</div></span>" +
"<span><div class=\"dataul\"> <h4>UniProt ID:</h4>" + "<a target=\"_blank\" href=http://purl.uniprot.org/uniprot/" + genes[i]['uniprot']['value'] + ">" + genes[i]['uniprot']['value'] + "</a>" + "</div></span>" +
"<span><div class=\"dataul\"> <h4>RefSeq Protein ID:</h4>" + "<a target=\"_blank\" href=https://www.ncbi.nlm.nih.gov/protein/" + genes[i]['refseqProtein']['value'] + ">" + genes[i]['refseqProtein']['value'] + "</a>" + "</div></span>" +
"<span><div class=\"dataul\"> <h4>Wikidata Item ID:</h4>" + "<a target=\"_blank\" href=" + genes[i]['protein']['value'] + ">" + protqid.slice(-1)[0] + "</a>" + "</div></span>"
);
$("#protbut").html("<button data-toggle=\"tooltip\" title=\"Go to the Wikidata page for the protein " + genes[i]['proteinLabel']['value'] + "\"" + "id=\"wdprotbut\" class=\"wdbutton btn btn-default\"><img id=\"wdlogo3\" src=\"img/GeneWikidata-logo-en.png\"></button>");
$('#wdprotbut').off("click").click(function () {
$(this).html("<a target=\"_blank\" href=" + prot_wd_uri + "> <img id=\"wdlogo3\" src=\"img/GeneWikidata-logo-en.png\"></a>");
});
}
}
$('#geneForm').val("");
});
}
});
});
});