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<!doctype html>
<html lang="en">
<head>
<meta charset="utf-8">
<title>PubMed xml to table bias</title>
<link rel="stylesheet" href="/openmetaanalysis.css">
<script src="//code.jquery.com/jquery-1.10.2.js"></script>
<script>
//http://www.alexhadik.com/blog/2014/6/12/create-pubmed-citations-automatically-using-pubmed-api
//http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&id=25164756&retmode=json
//http://api.jquery.com/jquery.getjson/
///Not used:
//http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2904758/
var citation_bias = '<?xml version=\"1.0\" encoding=\"UTF-8\"?><br><included><br>';
$(document).ready(function(){
$("#submitbutton").on("click", function(){
//disable the button to prevent multiple clicks
$("#submitbutton").prop( "disabled", true );
citation_data = ""
$("#status").html("<i>searching...</i>")
//Get list of IDs based on search terms
$.getJSON('http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&retmode=json',{
term : $("#input").val(),
format: "json"
})
.done(function(data){
var ids = data.esearchresult.idlist;
var publications = [];
iterateJSON(ids, publications);
$("#submitbutton").prop( "disabled", false );
});
});
function iterateJSON(idlist, publications) {
var id = idlist.pop();
// test with http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&id=11850928,11482001&format=json
$.getJSON('http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&id='+id+'&retmode=json',
function(summary){
var citation = "<span style='color:red;font-weight:bold'><!-- start of a new study --><br>";
//for(author in summary.result[id].authors){
// citation+=summary.result[id].authors[author].name+', ';
//}
//citation+=' \"'+summary.result[id].title+'\" <i>'+summary.result[id].fulljournalname+'</i> '+summary.result[id].volume+'.'+summary.result[id].issue+' ('+summary.result[id].pubdate+'): '+summary.result[id].pages+'.';
var studyname = summary.result[id].authors[0].name;
studyname = studyname.substring(0, studyname.indexOf(" "));
var pubyear = summary.result[id].pubdate
if (pubyear.indexOf(" ") > 1){
pubyear = pubyear.substring(0, pubyear.indexOf(" "));
}
if ($("#type_intervention").is(":checked")){
citation+="<study><br><citation year=\"" + pubyear + "\" pmid=\"" + summary.result[id].uid + '\" trialregistration=\"\" journal_abbrev=\"' + summary.result[id].source + '\" totalsubjects=\"0\" >' + studyname + "</citation></span><br>"
citation+= String.fromCharCode(9) + " <randomization <span style='background-color:green;color:white;font-weight:bold'>explanation=\"Method of randomization not described\"</span>><span style='background-color:yellow'>Unclear risk</span></randomization><br>"
citation+= String.fromCharCode(9) + " <allocation <span style='background-color:green;color:white;font-weight:bold'>explanation=\"Method of concealing allocation not stated\"</span>><span style='background-color:yellow'> risk</span></allocation><br>"
citation+= String.fromCharCode(9) + " <blinding_people <span style='background-color:green;color:white;font-weight:bold'>explanation=\"Did not state blinding of subjects and personnel.\"</span>><span style='background-color:yellow'> risk</span></blinding_people><br>"
citation+= String.fromCharCode(9) + " <blinding_assessment <span style='background-color:green;color:white;font-weight:bold'>explanation=\"Blinding of assessors not stated\"</span>><span style='background-color:yellow'>Unclear risk</span></blinding_assessment><br>"
citation+= String.fromCharCode(9) + " <attrition <span style='background-color:green;color:white;font-weight:bold'>explanation=\"Consort flow diagram not provided\"</span>><span style='background-color:yellow'>Unclear risk</span></attrition><br>"
citation+= String.fromCharCode(9) + " <selective_reporting <span style='background-color:green;color:white;font-weight:bold'>explanation=\"Original protocol not available at a website for trial registration.\"</span>><span style='background-color:yellow'>Unclear risk</span></selective_reporting><br>"
citation+= String.fromCharCode(9) + " <other_biases><span style='background-color:yellow'> risk</span></other_biases><br>"
citation+= "</study><br>"
$("#criteria").html("<a href=\"http://handbook-5-1.cochrane.org/chapter_8/table_8_5_d_criteria_for_judging_risk_of_bias_in_the_risk_of.htm\">Individual criteria for judging risk of bias</a> in a trial using the '<a href=\"http://handbook-5-1.cochrane.org/chapter_8/table_8_5_d_criteria_for_judging_risk_of_bias_in_the_risk_of.htm\">Cochrane's Risk of bias tool</a>'</li></ul>")
}
if ($("#type_diagnosis").is(":checked")){
citation+="<study><br><citation year=\"" + pubyear + "\" pmid=\"" + summary.result[id].uid + '\" nct=\"\" journal_abbrev=\"' + summary.result[id].source + '\" totalsubjects=\"0\" >' + studyname + "</citation></span><br>"
citation+= String.fromCharCode(9) + " <patient_selection <span style='background-color:green;color:white;font-weight:bold'>explanation=\"Nonconsecutive patients\"</span>><span style='background-color:yellow'>High risk</span></patient_selection><br>"
citation+= String.fromCharCode(9) + " <index_test><span style='background-color:yellow'> risk</span></index_test><br>"
citation+= String.fromCharCode(9) + " <reference_standard><span style='background-color:yellow'> risk</span></reference_standard><br>"
citation+= String.fromCharCode(9) + " <flow_timing><span style='background-color:yellow'> risk</span></flow_timing><br>"
citation+= "</study><br>"
$("#criteria").html("<a href=\"http://www.bris.ac.uk/quadas/quadas-2/\">Four criteria for judging risk of bias from QUADAS-2</a> (see Risk of bias row in the Table guided by the detailed criteria in the rows above)</li></ul>")
}
$("#hints").show()
//publications.push(citation);
publications += citation;
//citation = ""
//citation+="<span style='color:red;font-weight:bold'><citation pmid=\"" + summary.result[id].uid + '\" year=\"' + pubyear + '\" journal_abbrev=\"' + summary.result[id].source + '\">' + studyname + "</citation></span><br>";
//publications1.push(citation);
//citation = ""
//citation+=studyname + "," + pubyear + "," + summary.result[id].uid + ", , , , ,'',<br>";
//publications2.push(citation);
if(idlist.length!=0){
iterateJSON(idlist, publications);
}else{
//editor.setValue(publications)
$("#editor").html(citation_bias + publications + '<!-- Leave this bottom line --\><br></included>')
}
});
}
})
</script>
<style type="text/css" media="screen">
#editor {
position: relative;
border-style:solid;
border-width:medium;
}
#menu
{
list-style-type:none;
margin:0;
padding:0;
overflow:hidden;
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.listitem
{
display:inline;
float:left;
}
a.menuitem:link,a.menuitem:visited
{
display:block;
width:150px;
font-weight:bold;
text-align:center;
padding:4px;
text-decoration:none;background-color:#6DC6E7;
color:#FFFFFF;
}
a.menuitem:hover,a.menuitem:active
{
background-color:#0022B4;
color:#FFFFFF;
}
.tooltiptext{
display: none;
}
.ToolTipClass{
color:black;
border-color:#0022B4;
background-color: #6DC6E7
}
</style>
</head>
<body>
<!--
http://jquery-csv.googlecode.com/git/examples/basic-usage.html
http://jquery-csv.googlecode.com/git/examples/flot.html -> seems best and most stable without reticulating spines error
http://code.google.com/p/jquery-csv/wiki/API -> instructions
-->
<div class="wrapper">
<div class="page-header">
<div style="color:#0022B4">
<h1>openMetaAnalysis: <span style="font-size:50%">collaborative and continuous</span></h1>
</div>
<ul id="menu">
<li class="listitem"><a href="http://openmetaanalysis.github.io/" class="menuitem">Home</a></li>
<li class="listitem"><a href="https://public.opencpu.org/ocpu/github/openMetaAnalysis/home/www/editor.html" class="menuitem">Editor</a></li>
<li class="listitem"><a href="https://public.opencpu.org/ocpu/github/openMetaAnalysis/home/www/arrows.html" class="menuitem">Arrows Plot</a></li>
<li class="listitem"><a href="http://openmetaanalysis.github.io/methods.html" class="menuitem">Methods</a></li>
<li class="listitem"><a href="http://openmetaanalysis.github.io/contribute.html" class="menuitem">Get involved</a></li>
</ul>
</div>
<h2>Make tables</h2>
<input id="input" type="text" autocomplete="on" size="100" placeholder="Enter search terms or a list of PMIDs separated by spaces, commas, or semi-colons"><br/>
<button id="submitbutton" type="button">Submit</button>
<fieldset>
<legend style="font-weight:bold">Meta-analysis type</legend>
<div><input name="type" class="type" value="diagnosis" id="type_diagnosis" type="radio"><label for="type_diagnosis">Meta-analysis of diagnostic test assessments (DTAs)</label></div>
<div><input name="type" class="type" value="intervention" id="type_intervention" type="radio" checked><label for="type_intervention">Meta-analysis of randomized controlled trials (RCTs)</label></div>
</fieldset>
<div> </div>
<div id="status">Status: Waiting for input</div>
<h3>Risk of bias table</h3>
<div>Copy the content below into the appropriate file for topic. Then replace text that is highlighted in yellow using the criteria below:</div>
<div> </div>
<ul id="hints" style="display:none">
<li id="criteria"> </li>
<li id="explanations">For high and unclear risk, consider adding explanations as done in <span style="background-color:green;color:white;font-weight:bold">green</span> in example below. These will show when user mouses over the cell in the table.</li>
</ul>
<div id="editor">Please wait for code to be written here.</div>
<script>
//For gh-pages
//Page history and edit
var pagename = location.pathname.split('/').slice(-1);
if (pagename.toString().length < 1){pagename = "index.html"}
document.write("<div style='text-align:center'><a href='https://github.com/openMetaAnalysis/openMetaAnalysis.github.io/blob/master/" + pagename + "'>Edit this page</a> - <a href='https://github.com/openMetaAnalysis/openMetaAnalysis.github.io/commits/master/" + pagename + "'>Page history</a></div>")
</script>
</div>
<script src="javascripts/scale.fix.js"></script>
<script type="text/javascript">
var gaJsHost = (("https:" == document.location.protocol) ? "https://ssl." : "http://www.");
document.write(unescape("%3Cscript src='" + gaJsHost + "google-analytics.com/ga.js' type='text/javascript'%3E%3C/script%3E"));
</script>
<script type="text/javascript">
try {
var pageTracker = _gat._getTracker("UA-56740469-1");
pageTracker._trackPageview();
} catch(err) {}
</script>
</body>
</html>