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<!doctype html>
<html lang="en">
<head>
<meta charset="utf-8">
<title>PubMed xml to table PICO</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 );
$("#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 );
});
$("#hints").show()
});
$(".type").on("click", function(){
$("#labels").show()
if ($("#type_intervention").is(":checked")){
$("#box0label").html('Enter study design')
$("#box0").attr("placeholder", "Enter randomized controlled trial?")
$("#box1label").html('Patients')
$("#box1").attr("placeholder", "Enter the condition being studied")
$("#box2label").html('Intervention')
$("#box2").attr("placeholder", "Enter the intervention being studied")
$("#box3label").html('Comparison')
$("#box3").attr("placeholder", "Enter placebo?")
$("#box4label").html('Outcome')
$("#box4").attr("placeholder", "Enter the primary outcome being studied (your can add secondaires later)")
}
if ($("#type_diagnosis").is(":checked")){
$("#box0label").html('Enter study design')
$("#box0").attr("placeholder", "Enter cross sectional study (be careful of case-control)?")
$("#box1label").html('Patients')
$("#box1").attr("placeholder", "Enter sndrome or condition being studied")
$("#box2label").html('Index test')
$("#box2").attr("placeholder", "Enter the index test (test/symptom/sign) being studied")
$("#box3label").html('Reference test')
$("#box3").attr("placeholder", "Enter the reference ('gold standard') test")
$("#box4label").html('Flow and timing')
$("#box4").attr("placeholder", "Enter something like 'index preceded reference test by x to x days'")
}
});
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
$.getJSON('http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&id='+id+'&retmode=json',
function(summary){
var citation = "<span style='color:red;font-weight:bold'><!-- start of a new study --><br>";
//for(author in summary.result[id].authors){
// citation+=summary.result[id].authors[author].name+', ';
//}
//citation+=' \"'+summary.result[id].title+'\" <i>'+summary.result[id].fulljournalname+'</i> '+summary.result[id].volume+'.'+summary.result[id].issue+' ('+summary.result[id].pubdate+'): '+summary.result[id].pages+'.';
var studyname = summary.result[id].authors[0].name;
studyname = studyname.substring(0, studyname.indexOf(" "));
var pubyear = summary.result[id].pubdate
if (pubyear.indexOf(" ") > 1){
pubyear = pubyear.substring(0, pubyear.indexOf(" "));
}
citation+= "<study><br><citation year=\"" + pubyear + "\" pmid=\"" + summary.result[id].uid + '\" trialregistration=\"\" journal_abbrev=\"' + summary.result[id].source + '\">' + studyname + "</citation></span><br>"
if ($("#type_intervention").is(":checked")){
citation+= String.fromCharCode(9) + " <design><span style='background-color:yellow'>" + $("#box0").val() + "</span></design><br>"
citation+= String.fromCharCode(9) + " <patients total=\"<span style='background-color:yellow'>__</span>\"><br>"
citation+= String.fromCharCode(9) + " <description><span style='background-color:yellow'>" + $("#box1").val() + "</span></description><br>"
citation+= String.fromCharCode(9) + " <bullet><span style='background-color:yellow'>Mean age __ months</span></bullet><br>"
citation+= String.fromCharCode(9) + " </patients><br>"
citation+= String.fromCharCode(9) + " <intervention><span style='background-color:yellow'>" + $("#box2").val() + "</span><br>"
citation+= String.fromCharCode(9) + " <bullet><span style='background-color:yellow'>Amount?</span></bullet><br>"
citation+= String.fromCharCode(9) + " <bullet><span style='background-color:yellow'>Frequency?</span></bullet><br>"
citation+= String.fromCharCode(9) + " <bullet><span style='background-color:yellow'>Duration?</span></bullet><br>"
citation+= String.fromCharCode(9) + " </intervention><br>"
citation+= String.fromCharCode(9) + " <comparison><span style='background-color:yellow'>" + $("#box3").val() + "</span><br>"
citation+= String.fromCharCode(9) + " </comparison><br>"
citation+= String.fromCharCode(9) + " <outcome><br>"
citation+= String.fromCharCode(9) + " <bullet type='primary' url='http://pubmed.gov/delete_url_if_not_needed'><span style='background-color:yellow'>" + $("#box4").val() + " measured how and when</span></bullet><br>"
citation+= String.fromCharCode(9) + " <bullet type='secondary'><span style='background-color:yellow'>Criteria used or how measured?</span></bullet><br>"
citation+= String.fromCharCode(9) + " </outcome><br>"
$("#criteria").html("<a href=\"http://handbook.cochrane.org/chapter_8/table_8_5_d_criteria_for_judging_risk_of_bias_in_the_risk_of.htm\">Individual criteria for judging risk of bias</a> in a trial using the '<a href=\"http://handbook.cochrane.org/chapter_8/8_5_the_cochrane_collaborations_tool_for_assessing_risk_of_bias.htm\">Cochrane's Risk of bias tool</a>'</li></ul>")
}
if ($("#type_diagnosis").is(":checked")){
citation+= String.fromCharCode(9) + " <design><span style='background-color:yellow'>" + $("#box0").val() + "</span></design><br>"
citation+= String.fromCharCode(9) + " <patient_selection total=\"<span style='background-color:yellow'>__</span>\"><br>"
citation+= String.fromCharCode(9) + " <description><span style='background-color:yellow'>" + $("#box1").val() + "</span></description><br>"
citation+= String.fromCharCode(9) + " <bullet><span style='background-color:yellow'>Consecutive enrollment</span></bullet><br>"
citation+= String.fromCharCode(9) + " <bullet><span style='background-color:yellow'>Mean age __ months</span></bullet><br>"
citation+= String.fromCharCode(9) + " </patient_selection><br>"
citation+= String.fromCharCode(9) + " <index_test><span style='background-color:yellow'>" + $("#box2").val() + "</span><br>"
citation+= String.fromCharCode(9) + " <bullet><span style='background-color:yellow'>Who interpreted?</span></bullet><br>"
citation+= String.fromCharCode(9) + " <bullet><span style='background-color:yellow'>Interpretation standardized?</span></bullet><br>"
citation+= String.fromCharCode(9) + " </index_test><br>"
citation+= String.fromCharCode(9) + " <reference_standard><span style='background-color:yellow'>" + $("#box3").val() + "</span><br>"
citation+= String.fromCharCode(9) + " <bullet type='primary'><span style='background-color:yellow'>Criteria or cutoffs used?</span></bullet><br>"
citation+= String.fromCharCode(9) + " <bullet type='secondary' ><span style='background-color:yellow'>Who interpreted?</span></bullet><br>"
citation+= String.fromCharCode(9) + " <bullet type='secondary' url='http://pubmed.gov/delete_url_if_not_needed'><span style='background-color:yellow'>Interpretation standardized?</span></bullet><br>"
citation+= String.fromCharCode(9) + " </reference_standard><br>"
citation+= String.fromCharCode(9) + " <flow_timing><span style='background-color:yellow'>" + $("#box4").val() + "</span><br>"
citation+= String.fromCharCode(9) + " <bullet><span style='background-color:yellow'>Other issues to note?</span></bullet><br>"
citation+= String.fromCharCode(9) + " </flow_timing><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>")
}
citation+= "</study><br>"
//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;
}
.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" ><label for="type_intervention">Meta-analysis of randomized controlled trials (RCTs)</label></div>
</fieldset>
<fieldset id="labels" style="display:none">
<legend style="font-weight:bold">Prepopulate fields that are similar between studies?</legend>
<table style="border:none;border-collapse: collapse;">
<tr><td style="width:200px"><span id="box0label"> </span></td><td><input name="box0" class="field" placeholder="enter text" id="box0" size="100"></td></tr>
<tr><td style="width:200px"><span id="box1label"> </span></td><td><input name="box1" class="field" placeholder="enter condition being studied" id="box1" size="100"></td></tr>
<tr><td style="width:200px"><span id="box2label"> </span></td><td><input name="box2" class="field" placeholder="enter text" id="box2" size="100"></td></tr>
<tr><td style="width:200px"><span id="box3label"> </span></td><td><input name="box3" class="field" placeholder="enter text" id="box3" size="100"></td></tr>
<tr><td style="width:200px"><span id="box4label"> </span></td><td><input name="box4" class="field" placeholder="enter text" id="box4" size="100"></td></tr>
</table>
</fieldset>
<div id="status">Status: Waiting for input</div>
<h3>PICO table</h3>
<div>Copy the content below into the appropriate file for topic. Then replace text that is highlighted in yellow. Add text relevant to the criteria below:</div>
<ul id="hints" style="display:none">
<li id="bullets">If a bullet is not needed, delete its entire row.</li>
<li id="criteria"> </li>
<li id="explanations">For important clinical observations that may explain a study's results, consider surrounding the text with **<span style="background-color:yellow;">to make a yellow highlight</span>**.</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>