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xjtushilei committed Jun 24, 2017
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26 changes: 26 additions & 0 deletions .gitignore
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# Created by .ignore support plugin (hsz.mobi)
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# Reference: https://intellij-support.jetbrains.com/hc/en-us/articles/206544839
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# IntelliJ
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# mpeltonen/sbt-idea plugin
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206 changes: 206 additions & 0 deletions Ontology.html
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<!DOCTYPE html>
<html lang="en-US"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8">

<title>PDD Graph</title>
<meta name="description" content="MIMIC-III to Linked Data Cloud">
<meta name="viewport" content="width=device-width, initial-scale=1">
<meta name="theme-color" content="#157878">
<link href="css" rel="stylesheet" type="text/css">
<link rel="stylesheet" href="my/style.css">
</head>
<body style="position: static;">
<section class="page-header">
<h1 class="project-name"><a href="index.html" style="color: white">PDD Graph</a></h1>
<h2 class="project-tagline">PDD Graph is a Patient-Disease-Drug Graph, Bridging MIMIC-III and Linked Data Cloud.</h2>

<a href="index.html" class="btn">Introduction</a>
<a href="index.html#download" class="btn">Download</a>
<a href="index.html#sparql-endpoint" class="btn">Online Query</a>
<a href="Tutorial.html" class="btn">Tutorial</a>
<a href="Ontology.html" class="btn">Ontology</a>


</section>

<section class="main-content">


<h1 >Ontology</h1>

<h4>Last update</h4>

24 June 2017


<h4>Namespace URI</h4>

http:https://kmap.xjtudlc.com/pdd_data/



<h2>Ontology at a glance</h2>

<ul>
<li><a href="#Class" title="">Class</a></li>
<li><a href="#Property" title="">Property</a></li>
</ul>

<h3 id="Class">Class</h3>

<div>
<ul>
Hospitalized patients
<br>
class : <code>pdd_data/vocabulary:Patient</code>
<br>
URI : <code>http:https://kmap.xjtudlc.com/pdd_data/vocabulary:Patient</code>
</ul>
</div>


<div>
<ul>
Admission information
<br>
class : <code>pdd_data/vocabulary:Admission</code>
<br>
URI : <code>http:https://kmap.xjtudlc.com/pdd_data/vocabulary:Admission</code>
</ul>
</div>

<div>
<ul>
Drog information
<br>
class : <code>pdd_data/vocabulary:Drog</code>
<br>
URI : <code>http:https://kmap.xjtudlc.com/pdd_data/vocabulary:Drog</code>
</ul>
</div>

<div>
<ul>
Disease information
<br>
class : <code>pdd_data/vocabulary:Disease</code>
<br>
URI : <code>http:https://kmap.xjtudlc.com/pdd_data/vocabulary:Disease</code>
</ul>
</div>

<h3 id="Property">Property</h3>

<div>
<ul>
gender
<br>
class : <code>property/gender</code>
<br>
URI : <code>http:https://kmap.xjtudlc.com/pdd_data/property/gender</code>
</ul>
</div>

<div>
<ul>
age
<br>
class : <code>property/age</code>
<br>
URI : <code>http:https://kmap.xjtudlc.com/pdd_data/property/age</code>
</ul>
</div>

<div>
<ul>
hospital admission id
<br>
class : <code>property/hospital_admission_id</code>
<br>
URI : <code>http:https://kmap.xjtudlc.com/pdd_data/property/hospital_admission_id</code>
</ul>
</div>


<div>
<ul>
bmi(Body Mass Index) first
<br>
class : <code>property/bmi_first</code>
<br>
URI : <code>http:https://kmap.xjtudlc.com/pdd_data/property/bmi_first</code>
</ul>
</div>


<div>
<ul>
bmi(Body Mass Index) min
<br>
class : <code>property/bmi_min</code>
<br>
URI : <code>http:https://kmap.xjtudlc.com/pdd_data/property/bmi_min</code>
</ul>
</div>


<div>
<ul>
bmi(Body Mass Index) max
<br>
class : <code>property/bmi_max</code>
<br>
URI : <code>http:https://kmap.xjtudlc.com/pdd_data/property/bmi_max</code>
</ul>
</div>


<div>
<ul>
diagnoses icd9
<br>
class : <code>property/diagnoses_icd9</code>
<br>
URI : <code>http:https://kmap.xjtudlc.com/pdd_data/property/diagnoses_icd9</code>
</ul>
</div>


<div>
<ul>
take drug name
<br>
class : <code>property/take_drug_name</code>
<br>
URI : <code>http:https://kmap.xjtudlc.com/pdd_data/property/take_drug_name</code>
</ul>
</div>

<div>
<ul>
take drugbank id
<br>
class : <code>property/take_drugbank_id</code>
<br>
URI : <code>http:https://kmap.xjtudlc.com/pdd_data/property/take_drugbank_id</code>
</ul>
</div>

<div>
<ul>
patient id
<br>
class : <code>property/patient_id</code>
<br>
URI : <code>http:https://kmap.xjtudlc.com/pdd_data/property/patient_id</code>
</ul>
</div>








</section>
</body></html>
70 changes: 70 additions & 0 deletions Tutorial.html
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<!DOCTYPE html>
<html lang="en-US"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8">

<title>PDD Graph</title>
<meta name="description" content="MIMIC-III to Linked Data Cloud">
<meta name="viewport" content="width=device-width, initial-scale=1">
<meta name="theme-color" content="#157878">
<link href="css" rel="stylesheet" type="text/css">
<link rel="stylesheet" href="my/style.css">
</head>
<body style="position: static;">
<section class="page-header">
<h1 class="project-name"><a href="index.html" style="color: white">PDD Graph</a></h1>
<h2 class="project-tagline">PDD Graph is a Patient-Disease-Drug Graph, Bridging MIMIC-III and Linked Data Cloud.</h2>

<a href="index.html" class="btn">Introduction</a>
<a href="index.html#download" class="btn">Download</a>
<a href="index.html#sparql-endpoint" class="btn">Online Query</a>
<a href="Tutorial.html" class="btn">Tutorial</a>
<a href="Ontology.html" class="btn">Ontology</a>


</section>

<section class="main-content">


<h1 >Tutorial</h1>

<p>Our data set provides the sparql endpoint, so you can use any programming language to query, based on the HTTP protocol.</p>
<p>Below we provide examples of online queries or queries using a programming language such as Python, Java ...</p>


<h3>Sparql Examples</h3>

<h3>Online Query</h3>

<p>First, Open the <a href="http:https://kmap.xjtudlc.com/pdd/dataset.html?tab=query&ds=/pdd" target="_blank">website</a></p>

<p>Second, Enter your own query statement in the input box. By the way, you can use the examples we provide above.</p>

<img src="my/use.png" alt="">

<p>Next, you can get the results below.</p>

<img src="my/use2.png" alt="">


<h3>Coding by yourself</h3>

<p>No matter what language you use, you can send a <em>post request</em> to the endpoint with the unique parameter <em>query</em>, and you can get the answer.</p>

Sparql Endpoint Url (Request URL) : <em>http:https://kmap.xjtudlc.com/pdd/pdd/query</em> <br>
Request Method :<em> post</em> <br>
Parameter : <em>query </em> (Your Sparql query) <br>

<p>Python example: </p>

<img src="my/python.png" alt="python example">

<p>

<code>

</code>
</p>


</section>
</body></html>
83 changes: 83 additions & 0 deletions index.html
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<!DOCTYPE html>
<html lang="en-US"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8">

<title>PDD Graph</title>
<meta name="description" content="MIMIC-III to Linked Data Cloud">
<meta name="viewport" content="width=device-width, initial-scale=1">
<meta name="theme-color" content="#157878">
<link href="css" rel="stylesheet" type="text/css">
<link rel="stylesheet" href="my/style.css">
</head>
<body style="position: static;">
<section class="page-header">
<h1 class="project-name"><a href="index.html" style="color: white">PDD Graph</a></h1>
<h2 class="project-tagline">PDD Graph is a Patient-Disease-Drug Graph, Bridging MIMIC-III and Linked Data Cloud.</h2>

<a href="index.html" class="btn">Document</a>
<a href="index.html#download" class="btn">Download</a>
<a href="index.html#sparql-endpoint" class="btn">Online Query</a>
<a href="Tutorial.html" class="btn">Tutorial</a>
<a href="Ontology.html" class="btn">Ontology</a>
<a href="Ontology.html" class="btn">Ontology</a>



</section>

<section class="main-content">


<h1 id="Introduction">Introduction</h1>

<p>What is <strong>PDD Graph</strong> (Patient-Disease-Drug Graph):</p>

<p> Electronic medical records contain multi-format electronic medical data that consist of an abundance of medical knowledge. Facing with patients symptoms, experienced caregivers make right medical decisions based on their professional knowledge that accurately grasps relationships between symptoms, diagnosis, and treatments. We aim to capture these relationships by constructing a large and high-quality heterogeneous graph linking patients, diseases, and drugs (PDD) in EMRs.</p>

<p> Specifically, we extract important medical entities from MIMIC-III (Medical Information Mart for Intensive Care III) and automatically link them with the existing biomedical knowledge graphs, including ICD-9 ontology and DrugBank. The PDD graph presented is accessible on the Web via the SPARQL endpoint, and provides a pathway for medical discovery and applications, such as effective treatment recommendations.</p>

<p> A subgraph of PDD is illustrated in the followng figure to betterunderstand the PDD graph.</p>

<img src="my/simple-graph.png" alt="A subgraph of PDD">


<h1 id="download">Download</h1>

<p>You can download it from different places. We offer two different formats in this site .</p>
<h4><a href="data/pdd_nt.zip" >Format 1：N-Triples</a></h4>
RDF data files ended by <em>.nt</em>.
<h4><a href="data/pdd_jena_tdb.zip" >Format 2：Apache Jena</a></h4>
Formatted by Apache Jena TDB , you can user it in Jena API.

<h3>Download elsewhere</h3>
<ul>
<li><a href="https://datahub.io/dataset/pdd-graph" >Datahub </a></li>
</ul>

<h1 id="sparql-endpoint">Online Query</h1>

<p>We provide the online query function, you can click <a href="http:https://kmap.xjtudlc.com/pdd/dataset.html?tab=query&ds=/pdd" target="_blank"><strong>here</strong></a> to online query.</p>

<p>If you are unfamiliar with the SPARQL query or unfamiliar with online queries, we provide several simple examples in <a href="Tutorial.html" ><strong>Tutorial</strong></a>
.</p>

<h1>Friendly Link</h1>
<p>Our data uses other data, so we make a statement here.</p>

<ul>
<li><a href="https://mimic.physionet.org/" target="_blank" >MIMIC-III</a></li>
<li><a href="http:https://bio2rdf.org/" target="_blank" >Bio2RDF </a></li>
<li><a href="https://datahub.io/dataset/bio2rdf-drugbank" target="_blank" >DrugBank </a></li>
<li><a href="http:https://bioportal.bioontology.org/ontologies/ICD9CM" target="_blank" >ICD-9 ontology </a></li>
</ul>
<h1 id="License">License</h1>

<div class="" style=";text-align:center">
<a rel="license" href="http:https://creativecommons.org/licenses/by/4.0/"><img alt="Creative Commons License" style="border-width:0" src="https://i.creativecommons.org/l/by/4.0/88x31.png"></a><br>
<br>
This work is licensed under a <a rel="license" href="http:https://creativecommons.org/licenses/by/4.0/">Creative Commons Attribution 4.0 International License</a>.
</div>


</section>
</body>
</html>
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