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clinicaltrials
Commit 5c8b59fa authored by david Chavalarias's avatar david Chavalarias
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adapation for nma

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data/All/Distributional.gexf deleted 100644 → 0
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data/All_/Conditionnal.gexf deleted 100644 → 0
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data/All_/project_conf.json deleted 100755 → 0
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{
"Conditionnal.gexf": {
"node0": {
"name": "term",
"reldbs": {
"csv": {
"file": "../clinicaltrials.csv",
"qcols": ["title","abstract"],
"template": "bib_details"
}
}
}
}
}
data/Treatments_/project_conf.json deleted 100755 → 0
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{
"Conditionnal.gexf": {
"node0": {
"name": "term",
"reldbs": {
"csv": {
"file": "../clinicaltrials.csv",
"qcols": ["title","abstract"],
"template": "bib_details"
}
}
}
}
}
data/clinicaltrials.csv
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data/conditionnal/ClinicalTrials_c_2020_05_05.gexf 0 → 100644
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data/Treatments/project_conf.json → data/conditionnal/project_conf.json
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{
"Distributional.gexf": {
"ClinicalTrials_c_2020_05_05.gexf": {
"node0": {
"name": "term",
"reldbs": {
......
data/distributional/ClinicalTrials_d_2020_05_05.gexf 0 → 100644
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data/All/project_conf.json → data/distributional/project_conf.json
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{
"Distributionnal.gexf": {
"ClinicalTrials_d_2020_05_05.gexf": {
"node0": {
"name": "term",
"reldbs": {
......@@ -12,4 +12,3 @@
}
}
}
data/graphs.zip 0 → 100644
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File added
data/test/hit_templates/bib_details.html deleted 100644 → 0
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<li class="searchhit" title="$${score}">
<p>
<b>$${tit}</b>
by
<span class="author">$${au}</span>
,
<i>$${src}</i>
[$${date}]
</p>
<p>
<span class="hit-keywords">
$${kws}
</span>
<span class="hit-text">
$${txt}
</span>
</p>
</li>
data/test/legends.json deleted 100644 → 0
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{
"someOccs": {
"col": "gradient",
"n": 3,
"binmode": "samepop",
"legend": "Test Occurrences"
},
"country": {"col": "cluster" , "legend": "Country", "binmode": "off" },
"myValue": {
"col": "heatmap",
"n": 2,
"binmode": "samerange",
"legend": "Some Important Value"
}
}
data/test/mini.csv deleted 100644 → 0
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"title" "pubdate" "author" "journal" "keywords" "text"
"python is nice" "2001" "Asher,Lutz" "areview" "python, forest" "hic in Palatio prima urbi fundamenta ieci. arcem iam scelere emptam Sabini habent"
"python is cool" "2003" "-cc-" "areview" "python, ocean" "hic in Palatio prima urbi fundamenta ieci. arcem iam scelere emptam Sabini habent"
"scala is great" "2003" "Odersky" "areviewB" "scala, crop" "hic in Palatio prima urbi fundamenta ieci. arcem iam scelere emptam Sabini habent"
"php is expressive" "2005" "Nixon" "areview" "php, mysql" "hic in Palatio prima urbi fundamenta ieci. arcem iam scelere emptam Sabini habent"
"php is expressive2" "2010" "-bb-" "areviewB" "php, web" "hic in Palatio prima urbi fundamenta ieci. arcem iam scelere emptam Sabini habent"
"javascript rules the web" "2005" "someguy,anotherguy" "areviewC" "javascript, web" "hic in Palatio prima urbi fundamenta ieci. arcem iam scelere emptam Sabini habent"
"a cool article" "2008" "-dd-" "areview" "coolness, ecosystem" "hic in Palatio prima urbi fundamenta ieci. arcem iam scelere emptam Sabini habent"
"another cool article" "2001" "-aa-" "areview" "coastal, coolness" "hic in Palatio prima urbi fundamenta ieci. arcem iam scelere emptam Sabini habent"
"a js primer" "2004" "mandelbrot" "areviewC" "coolness, ecosystem, grain yield" "hic in Palatio prima urbi fundamenta ieci. arcem iam scelere emptam Sabini habent"
"a scala js primer" "2004" "somebody" "areviewC" "keyword, ecosystem, growth response" "hic in Palatio prima urbi fundamenta ieci. arcem iam scelere emptam Sabini habent"
data/test/mini.gexf deleted 100644 → 0
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<gexf xmlns="http://www.gexf.net/1.1draft" xmlns:viz="http://www.gephi.org/gexf/viz" version="1.1">
<graph defaultedgetype="undirected" type="static">
<attributes class="node" type="static">
<attribute id="0" title="category" type="string"> </attribute>
<attribute id="1" title="country" type="string"> </attribute>
<attribute id="2" title="myValue" type="string"> </attribute>
<attribute id="3" title="someOccs" type="string"> </attribute>
</attributes>
<nodes>
<node id="T::0" label="scalajs">
<viz:size value="1"/>
<attvalues>
<attvalue for="0" value="term"/>
<attvalue for="3" value="1798"/>
</attvalues>
</node>
<node id="T::1" label="scala">
<viz:size value="1"/>
<attvalues>
<attvalue for="0" value="term"/>
<attvalue for="3" value="1577"/>
</attvalues>
</node>
<node id="T::2" label="python">
<viz:size value="1"/>
<attvalues>
<attvalue for="0" value="term"/>
<attvalue for="3" value="19"/>
</attvalues>
</node>
<node id="T::3" label="javascript">
<viz:size value="1"/>
<attvalues>
<attvalue for="0" value="term"/>
<attvalue for="3" value="1032"/>
</attvalues>
</node>
<node id="T::4" label="php">
<viz:size value="1"/>
<attvalues>
<attvalue for="0" value="term"/>
<attvalue for="3" value="655"/>
</attvalues>
</node>
<node id="P::0" label="-bb-">
<viz:size value="1"/>
<attvalues>
<attvalue for="0" value="person"/>
<attvalue for="1" value="China"/>
<attvalue for="2" value="14.995"/>
</attvalues>
</node>
<node id="P::1" label="-aa-">
<viz:size value="1"/>
<attvalues>
<attvalue for="0" value="person"/>
<attvalue for="1" value="Bhutan"/>
<attvalue for="2" value="8.9572"/>
</attvalues>
</node>
<node id="P::2" label="-dd-">
<viz:size value="1"/>
<attvalues>
<attvalue for="0" value="person"/>
<attvalue for="1" value="Brazil"/>
<attvalue for="2" value="4.6753"/>
</attvalues>
</node>
<node id="P::3" label="-cc-">
<viz:size value="1"/>
<attvalues>
<attvalue for="0" value="person"/>
<attvalue for="1" value="France"/>
<attvalue for="2" value="0.8481"/>
</attvalues>
</node>
<node id="P::4" label="-cc-">
<viz:size value="1"/>
<attvalues>
<attvalue for="0" value="person"/>
<attvalue for="1" value="Poland"/>
<attvalue for="2" value="8.6959"/>
</attvalues>
</node>
</nodes>
<edges>
<!-- bipartite 1|1 -->
<edge id="1" source="T::1" target="P::1"/>
<edge id="2" source="T::1" target="P::2"/>
<edge id="3" source="T::2" target="P::3"/>
<edge id="4" source="T::3" target="P::2"/>
<edge id="5" source="T::3" target="P::3"/>
<edge id="6" source="T::4" target="P::0"/>
<edge id="7" source="T::4" target="P::3"/>
<edge id="8" source="T::1" target="P::4"/>
<edge id="9" source="T::4" target="P::4"/>
<!-- intra sem 1|0 -->
<edge id="10" source="T::2" target="T::3"/>
<edge id="11" source="T::3" target="T::4"/>
<edge id="12" source="T::0" target="T::1"/>
<edge id="13" source="T::0" target="T::3"/>
<!-- intra soc 0|1 -->
<edge id="14" source="P::0" target="P::1"/>
<edge id="15" source="P::1" target="P::2"/>
<edge id="16" source="P::2" target="P::3"/>
<edge id="17" source="P::1" target="P::4"/>
</edges>
</graph>
</gexf>
data/test/project_conf.json deleted 100644 → 0
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{
"mini.gexf": {
"node0": {
"name": "term",
"reldbs": {
"csv": {
"file": "mini.csv",
"qcols": ["title","keywords","text"],
"template": "bib_details"
},
"twitter": {}
}
},
"node1": {
"name": "person",
"reldbs": {
"csv": {
"file": "mini.csv",
"qcols": ["author"],
"template": "bib_details"
}
}
}
}
}
explorerjs.html deleted 100644 → 0
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<!doctype html>
<html lang="en">
<head>
<meta charset="utf-8">
<meta name="language" content='EN'>
<meta name="language" content='FR'>
<meta name="keywords" content="dataviz, graph, data exploration, sigmajs, tinawebjs, projectExplorer">
<meta name="copyright" content="ISCPIF - UPS 3611 CNRS - 2017">
<meta name="revised" content="2017-04-01/rloth">
<meta name="viewport" content="width=device-width, initial-scale=1">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<!-- ======================== -->
<title>TinaWebJS Graph Explorer</title>
<!-- ======================== -->
<!-- Fonts -->
<!-- Ubuntu Condensed
Widely available font (possibly available without this cdn request, actually).
Also condensed is good for labels in crowded graphs
-->
<!-- <link href="https://fonts.googleapis.com/css?family=Ubuntu+Condensed" rel="stylesheet" type='text/css'> -->
<!-- Droid Sans -->
<link href="https://fonts.googleapis.com/css?family=Droid+Sans" rel="stylesheet">
<!-- Roboto
Good for tweets if Helvetica is not present
-->
<link href="https://fonts.googleapis.com/css?family=Roboto" rel="stylesheet" type='text/css'>
<!-- Crete Round
Original *and* informative :) -->
<link href='https://fonts.googleapis.com/css?family=Crete+Round:400,400italic&subset=latin-ext' rel='stylesheet' type='text/css'>
<!-- Lora
"book" (roman style) + nice heading -->
<!-- <link href="https://fonts.googleapis.com/css?family=Lora:700" rel="stylesheet" type='text/css'> -->
<!-- Aref Ruqaa
"book" (light ornamental) + arabic support -->
<!-- <link href="https://fonts.googleapis.com/css?family=Aref+Ruqaa" rel="stylesheet" type='text/css'> -->
<!-- Sahitya & Gurajada
"book" (beautiful quality roman) + devanagari support + telugu -->
<link href="https://fonts.googleapis.com/css?family=Gurajada" rel="stylesheet">
<!-- <link href="https://fonts.googleapis.com/css?family=Sahitya" rel="stylesheet"> -->
<!-- Itim
cursive (refined and very readable but a bit too wide for us) + thai support -->
<!-- <link href="https://fonts.googleapis.com/css?family=Itim" rel="stylesheet" type='text/css'> -->
<!-- CSS -->
<link rel="stylesheet" href="twlibs3/jquery-3/jquery-ui-1.12.1/jquery-ui.min.css" media="screen">
<!-- NB bootstrap 3 not used for main grid (graph + bars) but inside the bars -->
<link rel="stylesheet" href="twlibs3/bootstrap-3/css/bootstrap.min.css" media="screen">
<link rel="stylesheet" href="twlibs3/freshslider/freshslider.css" media="screen">
<link rel="stylesheet" href="twlibs3/tweets/tweet.light.excerpt.css" />
<link rel="stylesheet" href="twlibs3/tweets/custom.css"/>
<link rel="stylesheet" href="twlibs/css/twjs.css">
<link rel="stylesheet" href="twlibs/css/twjs-mobile.css">
<link rel="stylesheet" href="twlibs/css/selection-panels.css">
<link rel="stylesheet" href="twlibs/css/selection-panels-mobile.css">
<link rel="stylesheet" href="twlibs/css/user_form.css" />
<link rel="shortcut icon" href="twlibs/img/favicon.ico" type="image/x-icon" />
<!-- JS -->
<!-- <script src="script.js"></script> -->
</head>
<body>
<a id='mainlogo' href="https://github.com/moma/ProjectExplorer"
class="navbar-higher twbrand-link"
title="Project Explorer">
<img src="twlibs/img/logo.png"
style="width:50px; position:absolute; top:-8px; left:-4px; z-index:5; overflow:visible;">
</a>
<div id="topbar" class="navbar navbar-default">
<div class="container">
<div class="navbar-collapse collapse" id="navbar-main">
<ul class="nav navbar-nav navbar-left">
<li style="margin-left:10px;">
<!-- name will be replaced by TW.conf.branding, link by TW.conf.brandingLink -->
<a href="#" class="navbar-middle navbar-brand twbrand-link">
<span id="twbrand">TinaWebJS</span>
</a>
</li>
<li class="disabled">
<a class="navbar-middle">
<span class="label label-default label-lg">MAP: <span id="maplabel"></span></span>
</a>
</li>
<li>
<a class="navbar-middle">
<span id="network" ></span>
</a>
</li>
</ul>
<ul class="nav navbar-nav">
<li>
<div id="log"></div>
</li>
<li>
<a>
<div id="gexfs"></div>
</a>
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
<li><a href="http://www.cnrs.fr" target="_blank"
class="navbar-higher"
title="CNRS">
<img src="twlibs/img/logo_cnrs_transparent.gif" height="23"></a></li>
<li><a href="http://iscpif.fr" target="_blank"
class="navbar-higher"
title="ISC-PIF">
<img src="twlibs/img/logo_ISCPIF_small.svg" height="23"></a></li>
</ul>
</div><!--navbar-main-->
</div><!--container-->
</div><!--navbar-fixed-top-->
<!-- ex-defaultop -->
<div id="toolbar" class="navbar navbar-default">
<div id="defaultop" class="container-fluid">
<div class="navbar-header">
<button id="toolbar-open" type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#left" aria-expanded="false" aria-controls="navbar">
<span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
</div>
<div id="left" class="navbar-collapse collapse">
<ul class="nav navbar-nav navbar">
<!--
<li>
<a>
<select id="aselector" onchange="console.log('salut monde')" class="selectpicker" data-style="btn btn-success btn-sm" data-width="auto">
<option value="Scholars" selected>Scholars</option>
<option value="Keywords">Keywords</option>
</select>
</a>
</li>
-->
<li>
<a>
<button type="button" id="changetype" class="btn btn-success btn-sm">Change<br>Type</button>
</a>
</li>
<li>
<a>
<button type="button" id="changelevel" class="btn btn-primary btn-sm" title="sélectionnez des sommets pour changer de niveau" disabled>Change<br>Level</button>
</a>
</li>
<!-- <li>
<a>
<button type="button" id="doTest" class="btn btn-sm">Run Test</button>
</a>
</li> -->
<li id="areacircle-size"><a>
Selector size<br>
<div id="unranged-value" class="settingslider"></div>
</a></li>
<li class="tworow-selectors">
<!-- Adjust the node sizes per nodetype-->
<table>
<tr class="for-nodecategory-0">
<td class="slider-legend">
Label Size
</td>
<td id="sliderlabelsize0" class="settingslider">
</td>
</tr>
<tr class="for-nodecategory-1">
<td class="slider-legend">
Label Size
</td>
<td id="sliderlabelsize1" class="settingslider">
</td>
</tr>
</table>
</li>
<li id="setcolorsMenu" class="dropdown">
<a class="dropdown-toggle" data-toggle="dropdown" href="#" role="button" aria-haspopup="true" aria-expanded="false">
Set Colors <img title="Set Colors" src="twlibs/img/colors.png" width="20px"><span class="caret"></span>
</a>
<ul id="colorgraph-menu" class="dropdown-menu">
</ul>
</a></li>
<li class="tworow-selectors for-nodecategory-0">
<!-- Create a subgraph over nodes from TW.categories[0] (terms or def nodes)-->
<table>
<tr>
<td class="slider-legend">
Nodes
</td>
<td id="slidercat0nodesweight" class="settingslider">
</td>
</tr>
<tr>
<td class="slider-legend">
Edges
</td>
<td id="slidercat0edgesweight" class="settingslider">
</td>
</tr>
</table>
</li>
<li class="tworow-selectors for-nodecategory-1">
<!-- Create a subgraph over nodes from TW.categories[1] (docs or people)-->
<table>
<tr class="weight-selector">
<td class="slider-legend">
Nodes
</td>
<td id="slidercat1nodesweight" class="settingslider">
</td>
</tr>
<tr class="weight-selector">
<td class="slider-legend">
Edges
</td>
<td id="slidercat1edgesweight" class="settingslider">
</td>
</tr>
</table>
</li>
</ul>
<ul id="searchnav" class='nav navbar-nav navbar-left'>
<li class="navbar-lower">
<div id="search_input_group" class="input-group input-group-sm my-nav-input-group">
<span class="input-group-btn crowdsourcingModule">
<button id="savesuggestion"
disabled
title="Save this topic as a new suggestion"
class="btn btn-default"
type="button">
<span class="glyphicon glyphicon-save"
id="saveicon">
</span>
</button>
</span>
<span class="input-group-btn">
<button id="searchbutton"
title="Search the topic in the map"
class="btn btn-primary"
type="button">
<span class="glyphicon glyphicon-search">
</span>
</button>
</span>
<!-- ########## THE SEARCH BAR ########## -->
<input id="searchinput"
type="text"
class="form-control"
placeholder="Select node(s)" />
<!-- strSearchBar will replace placeholder value -->
<!-- #################################### -->
</div>
</li>
<!-- messages below the search bar -->
<!-- say thanks for the suggestion, etc. -->
<li id="crowdsourcing_answer" class="nav crowdsourcingModule navbar-lower"></li>
<!-- checkbox -->
<li class="navbar-lower">
<table id="search_table">
<tr><td>
&nbsp;
<input id="checkboxdiv" onclick="alertCheckBox(this);"
title="Add next search results to current selection"
class="nav btn btn-info"
type="checkbox">
<!--span style="position: relative; top: 4px;">Add to selection</span-->
<span>Add to selection</span>
</td></tr>
<tr><td>
&nbsp;
<input type="radio" id="orop" name="search_operator" value="or"
checked>
<label for="orop">OR&nbsp;&nbsp;</label>
<input type="radio" id="andop" name="search_operator" value="and"
unchecked>
<label for="andop">AND</label>
</td></tr>
</table>
</li>
</ul>
</div><!-- /div#left -->
</div> <!-- /#defaultop -->
</div> <!-- /toolbar -->
</div>
<div id="sigma-contnr">
<div id="graph-panels">
<ul id="ctlzoom">
<!--
<li>
<a href="#" id="geomapicon" onclick="$('#geomapmodal').modal('show'); callGeomapADEME();">
<img title="World Map Distribution" width="34px" src="twlibs/img/world.png"></img>
</a>
</li>
-->
<li>
<a href="#" id="snapicon" onclick="saveGraphIMG();" class="zoombarbuttons">
<img title="Take a photo!" style="width:30px" src="twlibs/img/camera.png"></img>
</a>
</li>
<li>
<a href="#savemodal" id="saveAs" class="zoombarbuttons" data-toggle="modal" data-target="#savemodal">
<img style="width:28px" title="Save As..." src="twlibs/img/save.png"></img>
</a>
</li>
<li>
<a href="#" id="zoomPlusButton" title="Zoom In"> </a>
</li>
<li id="zoomSliderzone">
<div id="zoomSlider"></div>
</li>
<li>
<a href="#" id="zoomMinusButton" title="Zoom Out"> </a>
</li>
<li>
<a href="#" id="lensButton" class="zoombarbuttons"
title="Center View">
<img src="twlibs/img/target.png">
</a>
</li>
<li>
<a href="#" id="layoutButton" class="zoombarbuttons"
title="Force Atlas Layout">
<img src="twlibs/img/edges.png">
</a>
</li>
<li>
<a href="#" id="noverlapButton" class="zoombarbuttons"
title="Disperse Overlapping Nodes">
<img src="twlibs/img/disperse.png">
</a>
</li>
<li>
<a href="#facet-options" id="facets" class="zoombarbuttons"
title="Facets coloring options"
data-toggle="modal" data-target="#facet-options">
<img src="twlibs/img/facet_options.png"></img>
</a>
</li>
<li>
<div class="onoffswitch">
<input type="checkbox" name="edges-switch" class="onoffswitch-checkbox" id="edges-switch" checked>
<label class="onoffswitch-label" for="edges-switch">
<span id="edges-switch-inner-label" class="onoffswitch-inner"></span>
<span class="onoffswitch-switch"></span>
</label>
</div>
</li>
</ul>
<!-- inline *after* sigma-contnr for better overlay positioning -->
<!-- Sidebar top left -->
<div id="lefttopbox">
<!-- selected nodes -->
<div id="tw-current-selection">
<button id="unselectbutton" class="btn-xs"
onclick='cancelSelection(false);'
title="Unselect these terms">
<span class="glyphicon glyphicon-remove" alt="X"></span>
</button>
<div id="names"></div>
</div>
<!-- histogram of selected nodes -->
<div class="histogramModule">
<!-- filled by query (user search value) to wos api -->
<div id="search_histogram" class="over-panels"></div>
</div><!-- /row -->
<!-- histogram of selected nodes, variant ; TODO unify -->
<div class="histogramDailyVariantModule">
<!-- filled by query (user search value) to wos api -->
<div id="search_histogram2" class="over-panels"></div>
</div><!-- /row -->
</div>
<!-- attributes' legends (absolute position bottom left)
(contains one div of class "my-legend" per colored nodetype) -->
<div id="legend-for-facets" class="over-panels"></div>
<!-- to reopen the panel -->
<div id="sideunfold">
<img title="Open sidepanel" src="twlibs/img/unfold2.png"></img>
</div>
</div>
</div>
<div id="sidebar">
<!-- manual file chooser if run locally -->
<div id="localInput"></div>
<div id="selection-tabs-contnr" class='selection-tabs-contnr'>
<!-- selection's neighbors display -->
<ul class='etabs nav nav-tabs'>
<!-- for related elements from the combined graph (eg soc => sem) -->
<li id="taboppos" class='tab'>
<a href="#tagcloud-XR">Opposite-Neighbors</a>
</li>
<!-- for neighbors within this graph -->
<li id="tabsameside" class='tab'>
<a href="#tagcloud-00">Related</a>
</li>
</ul>
<div class='panel-container'>
<!-- 2 tabs with outer div for tabbing, inner div for readmore (readmore needs its container to be never hidden)-->
<div id="tagcloud-XR">
<div id="read-opposite-neighs"></div>
</div>
<div id="tagcloud-00">
<div id="read-sameside-neighs"></div>
</div>
</div>
</div>
<!-- topPapers tabs -->
<div id="reldocs-tabs-wrapper" class="reldocs">
<!-- NB: data-reldocstype should match TW.conf.relatedDocsType
and will be filled from TW.conf.relatedDocsAPIS keys
-->
<ul id="reldocs-tabs" class="nav nav-tabs" role="tablist">
</ul>
<!-- One tab pane
(only one with topPapers, we change content ourselves)
-->
<div id="reldocs-boxes" class="tab-content">
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exemple:
<div id="rd-0-csv" role="tabpanel" class="topPapers tab-pane active">
</div>
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<div id="information"></div>
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bottom right column as panels
open/close panel from: jsfiddle.net/KyleMit/kcpma
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&nbsp;Tutorial video
</a>
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</div>
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<p>here video</p>
<video width="100%"
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&nbsp;Tips
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<p>here tips inserted by twmain/Tinaweb.js</p>
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&nbsp;Credits
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<a href="https://bigdata.iscpif.fr/" target="_blank">
<img src="https://bigdata.iscpif.fr/images/logos/BIGDATA-Logo-PoweredBy-light.jpg"
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<a href="https://github.com/moma" target="_blank">
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alt="Sciencemapping"
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<div class="modal-content">
<div class="modal-header">
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<h4 class="modal-title">Exporting GEXF file</h4>
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What do you want to save?:
<div class="form-group">
<label class="col-lg-2 control-label"> </label>
<div class="col-lg-10">
<div class="radio">
<label>
<input type="radio" name="optionsRadios" id="fullgraph" value="option1" checked="true">
Full Graph
</label>
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Visible Graph
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<label class="col-lg-2 control-label"> </label>
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Size
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<div class="checkbox">
<label>
<input type="checkbox" name="optionsRadios" id="check_color" value="option2">
Color
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<!-- this titling functionality is like a head -n inside each class -->
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<label for="attr-titling-metric" class="smlabel input-group-addon">Titling metric</label>
<select id="attr-titling-metric" name="attr-titling-metric"
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</div>
<div class="input-group" style="margin-top:.5em;">
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>
</div>
</div>
</form>
</div>
</div>
<div class="modal-footer">
<button class="btn btn-default" data-dismiss="modal">
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</button>
<button class="btn btn-primary"
type=button onclick="newAttrConfAndColor()" data-dismiss="modal">
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</button>
</div>
</div>
</div>
</div>
<!--
<div id="geomapmodal" class="modal fade">
<div class="modal-header">
<button type="button" class="close" data-dismiss="modal" aria-hidden="true">×</button>
<h4 class="modal-title">Geomap</h4>
</div>
<div class="modal-body">
<div class="geomapCont"></div>
</div>
<div id="closegeomap" data-dismiss="modal"></div>
</div> -->
<!-- <div id="heatgraph"></div> -->
</div>
<!-- SCRIPTS -->
<script src="twlibs3/jquery-3/jquery-3.2.0.min.js" type="text/javascript"></script>
<script src="twlibs3/jquery-3/jquery-ui-1.12.1/jquery-ui.min.js" type="text/javascript"></script>
<script src="twlibs3/jquery-3/jquery.easytabs.js" type="text/javascript"></script>
<script src="twlibs3/freshslider/freshslider.1.0.js" type="text/javascript" ></script>
<script src="twlibs3/readmore.js" type="text/javascript"></script>
<script src="twlibs3/tweets/widgets.js" type="text/javascript" language="javascript"></script>
<script src="twlibs3/bootstrap-native/bootstrap-native.js"></script>
<!-- new sigma 1.2 imports -->
<!-- <script src="twlibs3/sigma_v1.2/sigma.min.js" type="text/javascript" language="javascript"></script> -->
<script src="twlibs3/sigma_v1.2/sigma.noIndexes.js" type="text/javascript" language="javascript"></script>
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NB: our sigma.noIndexes.js has exactly the same functions & varnames as
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<script src="twlibs3/sigma_v1.2/plugins/sigma.layout.forceAtlas2/supervisor.js"></script>
<script src="twlibs3/sigma_v1.2/plugins/sigma.layout.forceAtlas2/worker.js"></script>
<script src="twlibs3/sigma_v1.2/plugins/sigma.renderers.snapshot/sigma.renderers.snapshot.js"></script>
<script src="twlibs3/sigma_v1.2/plugins/sigma.plugins.dragNodes/sigma.plugins.dragNodes.js"></script>
<script src="twmain/globalUtils.js"></script>
<!-- new sigma (1.0c => 1.2) compatibility imports -->
<script src="twmain/sigma_tools.js"></script>
<!-- classic tinawebJS imports -->
<script src="settings_explorerjs.js"></script>
<script src="twmain/jLouvain.js"></script>
<script src="twmain/enviroment.js"></script>
<script src="twmain/sigma.parseCustom.js"></script>
<script src="twmain/sigmaUtils.js"></script>
<script src="twmain/extras_explorerjs.js"></script>
<script src="twmain/methods.js"></script>
<script src="twmain/Tinaweb.js"></script>
<script src="twmain/main.js"></script>
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</html>
images/coronavirus.svg 0 → 100644
View file @ 5c8b59fa
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index.html
View file @ 5c8b59fa
......@@ -12,7 +12,7 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<!-- ======================== -->
<title>Observatory of Coronavirus Clinical Trials</title>
<title>Mapping of Coronavirus Clinical Trials</title>
<!-- ======================== -->
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......@@ -75,10 +75,10 @@
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......@@ -95,7 +95,7 @@
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<h5><b>Select the map:</b></h5>
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......@@ -103,8 +103,8 @@
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<span id="network" ></span>
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<span id="network" ></span>
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......@@ -153,9 +153,9 @@
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......@@ -168,17 +168,26 @@
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__
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<li class="nav-item">
__
</li>
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<a>
......@@ -259,10 +268,7 @@
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<button id="savesuggestion"
......@@ -314,22 +320,27 @@
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<input type="radio" id="orop" name="search_operator" value="or"
checked>
<label for="orop">OR&nbsp;&nbsp;</label>
<label for="orop" class="slider-legend">OR&nbsp;&nbsp;</label>
<input type="radio" id="andop" name="search_operator" value="and"
unchecked>
<label for="andop">AND</label>
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</td></tr>
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&nbsp;À propos (FR)
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<h1>Cartographie des Essais Cliniques sur le Corona Virus</h1>
<h3>Principaux objectifs</h3>
<p>Une centaine d'essais cliniques sur COVID-19 ont été lancés en quelques semaines dans le monde entier. Les essais prévus, en cours ou terminés sont recensés par l'OMS et des épidémiologistes.
<p>La mise à disposition d'une vue synthétique de ces essais cliniques est essentielle pour la coordination de la communauté de recherche : pour explorer de nouvelles cibles thérapeutiques tout en évitant des études similaires.<p>
<p>C'est l'objectif de cette cartographie qui, basée sur la fouille de données textuelles des métadonnées de ces essais, permet de voir d'un coup d'œil toutes les pistes explorées par les essais cliniques an cours, passé ou prévus, les combinaisons de traitements, leurs principales catégories et les résultats attendus ou observés.<p>
<p>Ces cartes montrent comment l'ensemble des traitements considérés dans les essais cliniques de 2020, qu'ils soient en cours, prévus ou achevés ont été combinés dans les essais cliniques au niveau mondial. Deux termes sont liés sur la carte s'il existe une relation statistique entre eux dans l'ensemble des essais cliniques.
<h3>Deux types de cartes sont disponibles</h3>
<ul>
<li> La première carte à s'afficher, appelée conditionnelle, montre comment les traitements ont été combinés dans les essais cliniques. Le poids d'un lien entre deux traitements est la probabilité que l'un soit considéré avec l'autre dans un même bras d'essai clinique.
<li> L'autre carte, appelée distributionnelle, met en évidence les similarités dans les contextes d'utilisation de ces traitements. Elle établit ainsi des relations entre des traitements qui n'auraient peut-être pas été considérés ensemble dans un même bras d'essai clinique, mais qui ont été combinés de manière similaire à d'autres traitements.
</ul>
<p>La formule mathématique de ces mesures de proximité se trouve dans le <a href="https://iscpif.fr/gargantext/mesures-utilisees-dans-gargantext/" target="blank">la documentation de Gargantext</a>A>
<h3>Détails</h3>
<p>Ces cartes sont basées sur la base de données des études COVID randomisées fournies par l'OMS et prétraitées par un <a href="https://covid-nma.com/" target="blank">consortium international d'organismes de recherche</a> qui filtrent, nettoient et enrichissent l'ensemble des données. Nous l'avons obtenu dans le cadre d'une colaboration avec la <a href="http://www.mastercer.com/home/professors/professor-boutron/" target="blank">Pr Isabelle Boutron</a> (CRESS-UMR1153) et le <a href="https://compare.aphp.fr/l-etude/l-equipe.html" target="blank">Pr Philippe Ravaud</a> (APHP) le 5 mai 2020. L'objectif de cette base de données est d'informer sur les études en cours et d'explorer de nouvelles cibles thérapeutiques, en évitant les études similaires. Elle synthétise plus de 616 essais cliniques avec un total de 1491 bras sur les coronavirus. </p>
<p>Les essais cliniques sont tous préenregistrés et donc normalement validés sur le plan éthique ; cependant, certains n'ont pas encore commencé. <br/>En date du 5 mai 2020, 616 études au total ont été enregistrées. Cette base de données est un travail manuel, il peut donc y avoir quelques incohérences, elle a été enrichie avec les familles de traitement.
<p>Ces cartes ont été réalisées en utilisant <a href="http://gargantext.org" target="blank">Gargantext</a> le 6 mai 2020. Elles visent à donner une vue d'ensemble de toutes les études COVID randomisées mentionnées dans la base de données de l'OMS. Nous avons procédé à une exploration de texte sur la description des traitements et des résultats afin d'en déduire les principales catégories d'essais cliniques et leurs éventuelles complémentarités.</p>
La méthodologie est décrite <a href="https://iscpif.fr/gargantext/your-first-map/" target="blank">ici</a> </p>
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&nbsp;About
&nbsp;About (EN)
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<h1>Observatory of Coronavirus Clinical Trials</h1>
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<div class="panel-collapse collapse" id="le_tutorial">
<div class="modal-body form-horizontal">
<h1>Mapping of Coronavirus Clinical Trials</h1>
Last update : April 8 2020.
<h3>Main goals</h3>
<p>Several hundred clinical trials on COVID-19 were launched within a few weeks worldwide. Planned/ongoing/terminated trials are being tracked by WHO and physicians.</p>
......@@ -544,21 +600,20 @@
<p>This is the objective of this mapping which, based on textual data mining of the metadata of these trials, allows to see at a glance all the avenues explored by current and past clinical trials, the combinations of treatments, their main categories and the expected or observed results.<p>
<p>What you see are the main categories of treatments and outcomes and for each of them, the most related treatments and outcomes are highlighted. Two terms are linked on the map if there is a statistical relation in the set of clinical trials between them.</p>
<p>What you see are all the treatments that are being considered in 2020 clinical trials whether ongoing, planned or completed and how they have been combined in those trials. Two terms are linked on the map if there is a statistical relation in the set of clinical trials between them.</p>
<h3>Four maps are available</h3>
You can select one of four maps :
<h3>Two maps are available</h3>
<ul>
<li> Two maps based on the analysis of the treatment description alone, and two based on the analysis of the treatment and outcomes description,
<li> For each case, links can represent two different proximity measures (see below).
<li> One map, nammed conditionnal, show how treatments have been combinned in clinical trials. The weigh of a link between two treatments is the probability that one is considered with the other.
<li> The other map, nammed distributional, infers treatment that have been tested in the same clinical trials context. It thus make relations between treatments that might not have been considered together but that have been tested with roughly the same other treatments.
</ul>
<h3>Details</h3>
<p>These maps are based on database of randomized COVID studies provided by the WHO and pre-processed by an <a href="https://covid-nma.com/" target="blank">international collaboration of laboratories</a> that filter, clean, enrich the dataset. We got it from <a href="http://www.mastercer.com/home/professors/professor-boutron/" target="blank">Pr Isabelle Boutron</a> (CRESS-UMR1153) on April 8 2020. The aim of this database is to inform about current studies and explore new therapeutic targets, avoiding similar studies. It synthetises more than 600 clinical trials arms on coronavirus. </p>
<p>These maps are based on database of randomized COVID studies provided by the WHO and pre-processed by an <a href="https://covid-nma.com/" target="blank">international collaboration of laboratories</a> that filter, clean, enrich the dataset. We got it from <a href="http://www.mastercer.com/home/professors/professor-boutron/" target="blank">Pr Isabelle Boutron</a> (CRESS-UMR1153) on May 5 2020. The aim of this database is to inform about current studies and explore new therapeutic targets, avoiding similar studies. It synthetises more than 616 clinical trials with a total of 1491 arms on coronavirus. </p>
<p>These studies are all pre-recorded and therefore normally ethically validated; however, some have not yet begun. <br/>As of April 8 2020, a total of 274 studies have been recorded. This database is a manual work so there may be some inconsistencies, it has been enriched with the treatment families.</p>
<p>Clinical trials are all pre-recorded and therefore normally ethically validated; however, some have not yet begun. <br/>This clinical trials database is a manual work so some inconsistencies might remain.</p>
<p>These maps has been realized using <a href="http://gargantext.org" target="blank">Gargantext</a> on April 11 2020. They aim at giving a bird eye view of all the randomized COVID studies mentionned in the WHO database. We did text-mining on the treatment description and outcome descriptions to infer the main categories of clinical trials and their possible complementarities.</p>
<p>These maps has been realized using <a href="http://gargantext.org" target="blank">Gargantext</a> on May 6 2020. They aim at giving a bird eye view of all the randomized COVID studies mentionned in the WHO database. We did text-mining on the treatment description and outcome descriptions to infer the main categories of clinical trials and their possible complementarities.</p>
The methodology is described <a href="https://iscpif.fr/gargantext/your-first-map/" target="blank">here</a> </p>
<p>When you click on a term, the most related terms are displayed in a tag cloud on the right along with the details of the clinical trials that mention the most of the selected terms.</p>
......@@ -567,19 +622,69 @@
<p>In each graph, the node size is a fonction of the pagerank of the term in the graph.</p>
<p>The mathematical formula of these proximity measure can be found in the <a href="https://iscpif.fr/gargantext/mesures-utilisees-dans-gargantext/" target="blank">Gargantext documentation.</a>
<h4>Warning</h4>
<p>This map uses a CNRS open source tool that has been diverted from its original use for visualization examples (<a href="https://github.com/moma/ProjectExplorer">ProjectExplorer</a>). The display of documents associated with a selection on the map has a few bugs that we will try to correct if this way of presenting clinical trials proves useful for researchers and practitioners working on coronavirus.</p>
<h4>More about these maps</h4>
Please contact <a href="http://chavalarias.org" target="blank">David Chavalarias</a>, CNRS, Complex Systems Institute of Paris Île-de-France.
</div>
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<div class="panel panel-default" id="Cred">
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<a data-toggle="collapse" data-target="#credits" href="#credits"
data-parent="#varinfos-accordion">
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&nbsp;Crédits & données
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<div class="modal-body form-horizontal">
<h4>Pour en savoir plus sur ces cartes</h4>
<p>Cartes réalisées par <a href="http://chavalarias.org" target="blank">David Chavalarias</a>, (CNRS, <a href="http://iscpif.fr" target="blank">Institut des Systèmes Complexes de Paris Île-de-France)<a> avec <a href="http://gargantext.org" target="blank">Gargantext</a> et visualisées avec <a href="https://gitlab.iscpif.fr/davidchavalarias/clinicaltrials" target="blank">TinawebJS.</a></p>
<p>Les données sur les essais cliniques ont été collectées via le système d'enregistrement international des essais cliniques (ICTRP) de l’OMS; ; puis nettoyées et enrichies sous la direction du <a href="https://clinicalepidemio.fr/members-of-the-team/isabelle-boutron/">Professeur Isabelle Boutron</a> (CRESS - Univ. de Paris/INSERM) et du <a href="http://www.mastercer.com/home/professors/professor-ravaud/">Professeur Philippe Ravaud</a> (CRESS - Univ. de Paris/INSERM) dans le cadre du projet <i><a href="https://www.covid-nma.com/">Living mapping and living systematic review of Covid-19 studies</a></i>. </p>
<p>Le développement de <a href="http://gargantext.org" target="blank">Gargantext</a> est effectué à <a href="http://iscpif.fr" target="blank">l'ISC-PIF</a> sous la direction d'<a href="https://alexandre.delanoe.org" target="blank">Alexandre Delanoë</a>. Merci à Caroline Bligny (Univ. Grenoble-Alpes) pour l'aide sur l'amélioration de TinaWebJS.</p>
<p>Les graphes éditables proposés ici sont <a href"data/graphs.zip" target="blank">téléchargeables ici au format zip</a></p>
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title="CNRS">
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&nbsp;Navigation
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<p>here tips inserted by twmain/Tinaweb.js</p>
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<b>Last update:</b> May 7 2020 - 709 Clinical trials with arms : 263 Preventions, 1435 Treatments and 12 Post-treatments
</div>
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<div class="panel panel-default" id="video_explanationw">
<!-- TODO: outcloud the video for better stream+player -->
<div class="panel-collapse collapse panel-heading id="details_fr">
......
server_menu.json
View file @ 5c8b59fa
{
"data/Treatments_": [
"Conditionnal.gexf"
],"data/Treatments": [
"Distributional.gexf"
"data/conditionnal": [
"ClinicalTrials_c_2020_05_05.gexf"
],"data/distributional": [
"ClinicalTrials_d_2020_05_05.gexf"
],
"data/All_": [
"Conditionnal.gexf"
],
"data/All": [
"Distributional.gexf"
],
"first_project": "data/Treatments_"
"first_project": "data/conditionnal"
}
settings_explorerjs.js
View file @ 5c8b59fa
......@@ -7,7 +7,7 @@ TW.conf = (function(TW){
let TWConf = {}
TWConf.branding = 'Coronavirus Clinical Trials' // <--- name displayed in upper left
TWConf.brandingLink = 'https://iscpif.fr/projects/coronavirus-related-projects' // <--- link to "home"
TWConf.brandingLink = 'http://www.covid-nma.com/' // <--- link to "home"
// ==========================
......@@ -179,16 +179,16 @@ TW.conf = (function(TW){
// if fa2Available, the auto-run config:
TWConf.fa2Enabled= false; // fa2 auto-run at start and after graph modified ?
TWConf.fa2Milliseconds=4000; // duration of auto-run
TWConf.minNodesForAutoFA2 = 5 // graph size threshold to auto-run
TWConf.fa2Enabled= true; // fa2 auto-run at start and after graph modified ?
TWConf.fa2Milliseconds=1000; // duration of auto-run
TWConf.minNodesForAutoFA2 = 10000 // graph size threshold to auto-run
// Full-text search
// ----------------
TWConf.maxSearchResults = 10 // how many "top papers" to display
TWConf.maxSearchResults = 20 // how many "top papers" to display
TWConf.minLengthAutoComplete = 1 // how many chars to type for autocomp
TWConf.maxSuggestionsAutoComplete = 10 // how many suggestions by autocomp
TWConf.maxSuggestionsAutoComplete = 15 // how many suggestions by autocomp
TWConf.strSearchBar = "Search"
......
twlibs/css/twjs.css
View file @ 5c8b59fa
......@@ -20,6 +20,8 @@ html.waiting {
cursor: wait;
}
#sigma-contnr {
position: fixed;
top: 105px;
......@@ -314,7 +316,7 @@ ul.infoitems {
padding: 10px;
border: 1px solid #555;
border-radius: 0 4px 4px 4px;
background-color: #BBB;
background-color: #1a80b6;
display: block;
}
......@@ -422,3 +424,43 @@ ul.infoitems {
#search_table td label {
font-weight:normal;
}
/* custom fpr nma */
.navbar {
background-color: #1a80b6;
border: 0px solid transparent;
}
body {
color: #fff;
}
.navbar-default .navbar-nav > li > a {
color: #f0f0f0;
}
.btn-primary.disabled.focus, .btn-primary.disabled:focus, .btn-primary.disabled:hover, .btn-primary[disabled].focus, .btn-primary[disabled]:focus, .btn-primary[disabled]:hover, fieldset[disabled] .btn-primary.focus, fieldset[disabled] .btn-primary:focus, fieldset[disabled] .btn-primary:hover {
background-color: #288008;
}
.btn-primary {
background-color: #0f3739;
}
.btn-sm{
margin-left: ($spacer * .5) !important;
}
body {
color: #1a80b6;
}
.slider-legend{
color: #f0f0f0;
}
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