Renamed SemSim lesson from numbered to named

Duke-GCB · Oct 2, 2024 · 9d476c8 · 9d476c8
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diff --git a/Lesson-09.qmd → Lesson-Semsim.qmd b/Lesson-09.qmd → Lesson-Semsim.qmd
@@ -2,7 +2,7 @@
 title: "Biostat 823 - Semantic Similarity"
 author: "Hilmar Lapp"
 institute: "Duke University, Department of Biostatistics & Bioinformatics"
-date: "Nov 28, 2023"
+date: "Oct 3, 2024"
 format:
   revealjs:
     slide-number: true
@@ -43,7 +43,7 @@ knitr:
 
 ## Common and disjoint ancestors
 
-![_I_ and _D_ are sometimes referred to as "disjoint common subsumers", i.e., the common subsumers that do not subsume another common subsumer. ](images/Semsim/concept-dag-subAll.svg){fig-align="center"}
+![_I_ and _D_ are examples of what is sometimes referred to as "disjoint common subsumers", i.e., the common subsumers that do not subsume another common subsumer. ](images/Semsim/concept-dag-subAll.svg){fig-align="center"}
 
 ## Pairwise semantic similarity {.smaller}
 

diff --git a/pub/Lesson-09.html → pub/Lesson-Semsim.html b/pub/Lesson-09.html → pub/Lesson-Semsim.html
@@ -1,23 +1,23 @@
 <!DOCTYPE html>
 <html lang="en"><head>
-<script src="Lesson-09_files/libs/clipboard/clipboard.min.js"></script>
-<script src="Lesson-09_files/libs/quarto-html/tabby.min.js"></script>
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-<link href="Lesson-09_files/libs/quarto-html/quarto-syntax-highlighting.css" rel="stylesheet" id="quarto-text-highlighting-styles"><meta charset="utf-8">
+<script src="Lesson-Semsim_files/libs/clipboard/clipboard.min.js"></script>
+<script src="Lesson-Semsim_files/libs/quarto-html/tabby.min.js"></script>
+<script src="Lesson-Semsim_files/libs/quarto-html/popper.min.js"></script>
+<script src="Lesson-Semsim_files/libs/quarto-html/tippy.umd.min.js"></script>
+<link href="Lesson-Semsim_files/libs/quarto-html/tippy.css" rel="stylesheet">
+<link href="Lesson-Semsim_files/libs/quarto-html/light-border.css" rel="stylesheet">
+<link href="Lesson-Semsim_files/libs/quarto-html/quarto-html.min.css" rel="stylesheet" data-mode="light">
+<link href="Lesson-Semsim_files/libs/quarto-html/quarto-syntax-highlighting.css" rel="stylesheet" id="quarto-text-highlighting-styles"><meta charset="utf-8">
   <meta name="generator" content="quarto-1.3.353">
 
   <meta name="author" content="Hilmar Lapp">
-  <meta name="dcterms.date" content="2023-11-28">
+  <meta name="dcterms.date" content="2024-10-03">
   <title>Biostat 823 - Semantic Similarity</title>
   <meta name="apple-mobile-web-app-capable" content="yes">
   <meta name="apple-mobile-web-app-status-bar-style" content="black-translucent">
   <meta name="viewport" content="width=device-width, initial-scale=1.0, maximum-scale=1.0, user-scalable=no, minimal-ui">
-  <link rel="stylesheet" href="Lesson-09_files/libs/revealjs/dist/reset.css">
-  <link rel="stylesheet" href="Lesson-09_files/libs/revealjs/dist/reveal.css">
+  <link rel="stylesheet" href="Lesson-Semsim_files/libs/revealjs/dist/reset.css">
+  <link rel="stylesheet" href="Lesson-Semsim_files/libs/revealjs/dist/reveal.css">
   <style>
     code{white-space: pre-wrap;}
     span.smallcaps{font-variant: small-caps;}
@@ -31,11 +31,11 @@
       vertical-align: middle;
     }
   </style>
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-  <link href="Lesson-09_files/libs/revealjs/plugin/quarto-line-highlight/line-highlight.css" rel="stylesheet">
-  <link href="Lesson-09_files/libs/revealjs/plugin/reveal-menu/menu.css" rel="stylesheet">
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-  <link href="Lesson-09_files/libs/revealjs/plugin/quarto-support/footer.css" rel="stylesheet">
+  <link rel="stylesheet" href="Lesson-Semsim_files/libs/revealjs/dist/theme/quarto.css">
+  <link href="Lesson-Semsim_files/libs/revealjs/plugin/quarto-line-highlight/line-highlight.css" rel="stylesheet">
+  <link href="Lesson-Semsim_files/libs/revealjs/plugin/reveal-menu/menu.css" rel="stylesheet">
+  <link href="Lesson-Semsim_files/libs/revealjs/plugin/reveal-menu/quarto-menu.css" rel="stylesheet">
+  <link href="Lesson-Semsim_files/libs/revealjs/plugin/quarto-support/footer.css" rel="stylesheet">
   <style type="text/css">
 
   .callout {
@@ -339,7 +339,7 @@ <h1 class="title">Biostat 823 - Semantic Similarity</h1>
     </div>
 </div>
 
-  <p class="date">2023-11-28</p>
+  <p class="date">2024-10-03</p>
 </section>
 <section id="semantic-similarity" class="slide level2 smaller">
 <h2>Semantic similarity</h2>
@@ -376,7 +376,7 @@ <h2>Common and disjoint ancestors</h2>
 <section id="common-and-disjoint-ancestors-1" class="slide level2">
 <h2>Common and disjoint ancestors</h2>
 
-<img data-src="images/Semsim/concept-dag-subAll.svg" class="r-stretch quarto-figure-center"><p class="caption"><em>I</em> and <em>D</em> are sometimes referred to as “disjoint common subsumers”, i.e., the common subsumers that do not subsume another common subsumer.</p></section>
+<img data-src="images/Semsim/concept-dag-subAll.svg" class="r-stretch quarto-figure-center"><p class="caption"><em>I</em> and <em>D</em> are examples of what is sometimes referred to as “disjoint common subsumers”, i.e., the common subsumers that do not subsume another common subsumer.</p></section>
 <section id="pairwise-semantic-similarity" class="slide level2 smaller">
 <h2>Pairwise semantic similarity</h2>
 <ul>
@@ -578,19 +578,19 @@ <h2>Further reading</h2>
   </div>
 
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-  <script src="Lesson-09_files/libs/revealjs/dist/reveal.js"></script>
+  <script src="Lesson-Semsim_files/libs/revealjs/dist/reveal.js"></script>
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+  <script src="Lesson-Semsim_files/libs/revealjs/plugin/quarto-line-highlight/line-highlight.js"></script>
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+  <script src="Lesson-Semsim_files/libs/revealjs/plugin/quarto-support/support.js"></script>
 
 
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+  <script src="Lesson-Semsim_files/libs/revealjs/plugin/notes/notes.js"></script>
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diff --git a/...bs/revealjs/plugin/reveal-menu/plugin.yml → ...bs/revealjs/plugin/reveal-menu/plugin.yml b/...bs/revealjs/plugin/reveal-menu/plugin.yml → ...bs/revealjs/plugin/reveal-menu/plugin.yml
diff --git a/...vealjs/plugin/reveal-menu/quarto-menu.css → ...vealjs/plugin/reveal-menu/quarto-menu.css b/...vealjs/plugin/reveal-menu/quarto-menu.css → ...vealjs/plugin/reveal-menu/quarto-menu.css
diff --git a/...evealjs/plugin/reveal-menu/quarto-menu.js → ...evealjs/plugin/reveal-menu/quarto-menu.js b/...evealjs/plugin/reveal-menu/quarto-menu.js → ...evealjs/plugin/reveal-menu/quarto-menu.js
diff --git a/...les/libs/revealjs/plugin/search/plugin.js → ...les/libs/revealjs/plugin/search/plugin.js b/...les/libs/revealjs/plugin/search/plugin.js → ...les/libs/revealjs/plugin/search/plugin.js
diff --git a/...libs/revealjs/plugin/search/search.esm.js → ...libs/revealjs/plugin/search/search.esm.js b/...libs/revealjs/plugin/search/search.esm.js → ...libs/revealjs/plugin/search/search.esm.js
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diff --git a/...files/libs/revealjs/plugin/zoom/plugin.js → ...files/libs/revealjs/plugin/zoom/plugin.js b/...files/libs/revealjs/plugin/zoom/plugin.js → ...files/libs/revealjs/plugin/zoom/plugin.js
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diff --git a/...9_files/libs/revealjs/plugin/zoom/zoom.js → ...m_files/libs/revealjs/plugin/zoom/zoom.js b/...9_files/libs/revealjs/plugin/zoom/zoom.js → ...m_files/libs/revealjs/plugin/zoom/zoom.js