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resources.html
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---
title: Resources
layout: main
---
<nav class="navbar navbar-expand-lg navbar-dark bg-primary fixed-top" id="sideNav">
<a class="navbar-brand js-scroll-trigger" href="#page-top">
<span class="d-block d-lg-none"></span>
</a>
<button class="navbar-toggler" type="button" data-toggle="collapse" data-target="#navbarSupportedContent"
aria-controls="navbarSupportedContent" aria-expanded="false" aria-label="Toggle navigation">
<span class="navbar-toggler-icon"></span>
</button>
<div class="collapse navbar-collapse" id="navbarSupportedContent">
<ul class="navbar-nav">
<li class="nav-item">
<a class="nav-link js-scroll-trigger" href="{{'' | absolute_url}}">Home</a>
</li>
<li class="nav-item">
<a class="nav-link js-scroll-trigger" href="#">Top of Page</a>
</li>
<li class="nav-item">
<a class="nav-link js-scroll-trigger" href="#ont">Ontologies</a>
</li>
<li class="nav-item">
<a class="nav-link js-scroll-trigger" href="#source">Source Code</a>
</li>
<li class="nav-item">
<a class="nav-link js-scroll-trigger" href="#semantic">Semantic Annotations</a>
</li>
<li class="nav-item">
<a class="nav-link js-scroll-trigger" href="#kg">Knowledge Graph Fragments</a>
</li>
<li class="nav-item">
<a class="nav-link js-scroll-trigger" href="#query">SPARQL Queries</a>
</li>
<li class="nav-item">
<a class="nav-link js-scroll-trigger" href="#reasoning">Reasoning Models</a>
</li>
</ul>
</div>
</nav>
<section id="ont">
<h2>Ontologies</h2><br/>
<div class="list-group">
<!--<a href="http://bioportal.bioontology.org/ontologies/CST" class="list-group-item">Cancer
Staging Terms <i class="fa fa-arrow-circle-right"></i> <small>http://bioportal.bioontology.org/ontologies/CST</small></a>
<a href="http://bioportal.bioontology.org/ontologies/BCS7" class="list-group-item">Breast Cancer
Staging Ontology for the AJCC 7<sup>th</sup> Edition <i class="fa fa-arrow-circle-right"></i> <small>http://bioportal.bioontology.org/ontologies/BCS7</small></a>
<a href="http://bioportal.bioontology.org/ontologies/BCS8" class="list-group-item">Breast Cancer
Staging Ontology for the AJCC 8<sup>th</sup> Edition <i class="fa fa-arrow-circle-right"></i> <small>http://bioportal.bioontology.org/ontologies/BCS8</small></a>
--></div>
<br/><br/>
</section>
<section id="source">
<h2>Source Code</h2><br/>
<a href="https://github.com/tetherless-world/SemanticDataDictionary" class="list-group-item">sdd2rdf</a>
<!-- <a href="./breast-cancer-staging/ajcc_r8_annotated_guideline_extractor" class="list-group-item">AJCC
Guideline Extractor</a>
<a href="./breast-cancer-staging/create_owl_axioms.py" class="list-group-item">OWL Axiom Generator</a>
<a href="./heals2vis/heals2vis/inferencer.py" class="list-group-item">Whyis Inference Agent</a>
<a href="./breast-cancer-staging/inference_rules.txt" class="list-group-item">Custom Inference Rules</a>
<a href="./heals2vis" class="list-group-item">Visualization</a>
--><br/><br/>
</section>
<section id="semantic">
<h2>Semantic Annotations</h2><br/>
<h3>Dictionary Mappings</h3><br/>
<div class="list-group list-group-item"> National Health and Nutrition Examination Survey (NHANES)
<a href="sdd_resources/NHANES/input/DM/DEMO_H_Doc-DM.csv" class="list-group-item">Demographics Dictionary Mappings</a>
<a href="sdd_resources/NHANES/input/DM/BMX_H_Doc-DM.csv" class="list-group-item">Birth Measures Dictionary Mappings</a>
<a href="sdd_resources/NHANES/input/DM/BPX_H_Doc-DM.csv" class="list-group-item">Blood Pressure Dictionary Mappings</a>
</div>
<div class="list-group list-group-item"> The Genomic Cancer Atlas (TCGA) through the Genomic Data Commons (GDC)
<a href="sdd_resources/TCGA-GDC/Clinical/input/DM/GDC_Clinical_DM.csv" class="list-group-item">Clinical Dictionary Mappings</a>
<a href="sdd_resources/TCGA-GDC/CNV/input/DM/GDC_CNV_DM.csv" class="list-group-item">Copy Number Variation (CNV) Dictionary Mappings</a>
<a href="sdd_resources/TCGA-GDC/EXP/input/DM/GDC_Exp_miRNA_DM.csv" class="list-group-item">miRNA Experiment Dictionary Mappings</a>
<a href="sdd_resources/TCGA-GDC/Methylation/input/DM/GDC_Methylation_DM.csv" class="list-group-item">Methylation Dictionary Mappings</a>
</div>
<h3>Codebooks</h3><br/>
<div class="list-group list-group-item"> National Health and Nutrition Examination Survey (NHANES)
<a href="sdd_resources/NHANES/input/CB/DEMO_H_Doc-CB.csv" class="list-group-item">Demographics Dictionary
Mappings</a>
<a href="sdd_resources/NHANES/input/CB/BMX_H_Doc-CB.csv" class="list-group-item">Birth Measures Codebook</a>
<a href="sdd_resources/NHANES/input/CB/BPX_H_Doc-CB.csv" class="list-group-item">Blood Pressure Codebook</a>
</div>
<div class="list-group list-group-item"> The Genomic Cancer Atlas (TCGA) through the Genomic Data Commons (GDC)
<a href="sdd_resources/TCGA-GDC/Clinical/input/CB/GDC_Clinical_CB.csv" class="list-group-item">Clinical Codebook</a>
<a href="sdd_resources/TCGA-GDC/CNV/input/CB/GDC_CNV_CB.csv" class="list-group-item">Copy Number Variation (CNV) Codebook</a>
<a href="sdd_resources/TCGA-GDC/EXP/input/CB/GDC_Exp_miRNA_CB.csv" class="list-group-item">miRNA Codebook</a>
<a href="sdd_resources/TCGA-GDC/Methylation/input/CB/GDC_Methylation_CB.csv" class="list-group-item">Methylation Codebook</a>
</div>
<!--<div class="list-group list-group-item"> CIViC
<a href="./RPI-HEALS-Semantic-Data-Dictionaries/CIVIC/civicDM.csv" class="list-group-item">Dictionary
Mappings</a>
<a href="./RPI-HEALS-Semantic-Data-Dictionaries/CIVIC/civicCB.csv" class="list-group-item">Code
Book</a>
</div>
<br/>
<i>
For the conversion to RDF using these files, please refer to the <a
href="https://github.com/tetherless-world/SemanticDataDictionary">Semantic Data Dictionary
specification</a>.
</i>
--><br/><br/>
</section>
<section id="kg">
<h2>Knowledge Graph Fragments</h2><br/>
<div class="list-group list-group-item"> National Health and Nutrition Examination Survey (NHANES)
<a href="sdd_resources/NHANES/output/trig/demo-kg.trig" class="list-group-item">Demographics KG Fragment</a>
<a href="sdd_resources/NHANES/output/trig/bmx-kg.trig" class="list-group-item">Birth Measures KG Fragment</a>
<a href="sdd_resources/NHANES/output/trig/bpx-kg.trig" class="list-group-item">Blood Pressure KG Fragment</a>
</div>
<div class="list-group list-group-item"> The Genomic Cancer Atlas (TCGA) through the Genomic Data Commons (GDC)
<a href="sdd_resources/TCGA-GDC/Clinical/output/trig/GDC_Clinical.trig" class="list-group-item">Clinical KG Fragment</a>
<a href="sdd_resources/TCGA-GDC/CNV/output/trig/GDC_CNV.trig" class="list-group-item">Copy Number Variation (CNV) KG Fragment</a>
<a href="sdd_resources/TCGA-GDC/EXP/output/trig/GDC_Exp_miRNA.trig" class="list-group-item">miRNA KG Fragment</a>
<a href="sdd_resources/TCGA-GDC/Methylation/output/trig/GDC_Methylation.trig" class="list-group-item">Methylation KG Fragment</a>
</div>
</section>
<section id="query">
<h2>Queries</h2><br/>
<div class="list-group list-group-item"> National Health and Nutrition Examination Survey (NHANES)
<a href="sdd_resources/NHANES/output/sparql/demoQuery" class="list-group-item">Demographics SPARQL Query</a>
<a href="sdd_resources/NHANES/output/sparql/bmxQuery" class="list-group-item">Birth Measures SPARQL Query</a>
<a href="sdd_resources/NHANES/output/sparql/bpxQuery" class="list-group-item">Blood Pressure SPARQL Query</a>
</div>
<div class="list-group list-group-item"> The Genomic Cancer Atlas (TCGA) through the Genomic Data Commons (GDC)
<a href="sdd_resources/TCGA-GDC/Clinical/output/sparql/GDC_Clinical_Q" class="list-group-item">Clinical SPARQL Query</a>
<a href="sdd_resources/TCGA-GDC/CNV/output/sparql/GDC_CNV_Q" class="list-group-item">Copy Number Variation (CNV) SPARQL Query</a>
<a href="sdd_resources/TCGA-GDC/EXP/output/sparql/GDC_Exp_miRNA_Q" class="list-group-item">miRNA SPARQL Query</a>
<a href="sdd_resources/TCGA-GDC/Methylation/output/sparql/GDC_Methylation_Q" class="list-group-item">Methylation SPARQL Query</a>
</div>
</section>
<section id="reasoning">
<h2>Reasoning Models</h2><br/>
<div class="list-group list-group-item"> National Health and Nutrition Examination Survey (NHANES)
<a href="sdd_resources/NHANES/output/sparql/demoSWRL" class="list-group-item">Demographics SWRL Antecedent</a>
<a href="sdd_resources/NHANES/output/sparql/bmxSWRL" class="list-group-item">Birth Measures SWRL Antecedent</a>
<a href="sdd_resources/NHANES/output/sparql/bpxSWRL" class="list-group-item">Blood Pressure SWRL Antecedent</a>
</div>
<div class="list-group list-group-item"> The Genomic Cancer Atlas (TCGA) through the Genomic Data Commons (GDC)
<a href="sdd_resources/TCGA-GDC/Clinical/output/swrl/GDC_Clinical_SWRL" class="list-group-item">Clinical SWRL Antecedent</a>
<a href="sdd_resources/TCGA-GDC/CNV/output/swrl/GDC_CNV_SWRL" class="list-group-item">Copy Number Variation (CNV) SWRL Antecedent</a>
<a href="sdd_resources/TCGA-GDC/EXP/output/swrl/GDC_Exp_miRNA_SWRL" class="list-group-item">miRNA SWRL Antecedent</a>
<a href="sdd_resources/TCGA-GDC/Methylation/output/swrl/GDC_Methylation_SWRL" class="list-group-item">Methylation SWRL Antecedent</a>
</div>
</section>