From 45219950b699d001e0a3b77861854e759d0280af Mon Sep 17 00:00:00 2001
From: Chris Sobczak <chris@sobczak.family>
Date: Fri, 8 May 2026 14:32:55 -0700
Subject: Add glossaries and adjust template stuff like was done for rmd

---
 lit-review-template.qmd | 30 +++++++++++++++++++++++-------
 1 file changed, 23 insertions(+), 7 deletions(-)

diff --git a/lit-review-template.qmd b/lit-review-template.qmd
index 3329a3d..f83bbc3 100644
--- a/lit-review-template.qmd
+++ b/lit-review-template.qmd
@@ -1,8 +1,8 @@
 ---
-title: "TEMPLATE_FIELD"
-author: "TEMPLATE_FIELD"
+title: "TITLE"
+author: "AUTHOR"
 date: now
-date-format: "DD MMMM YYYY - HH:mm"
+date-format: "MMMM DD YYYY"
 format:
   pdf:
     toc: false
@@ -12,14 +12,20 @@ format:
     include-in-header:
     - text: |
         \usepackage{etoolbox}
+        \usepackage[colorlinks=true,linkcolor=purple]{hyperref}
+        \usepackage[toc,acronym,automake]{glossaries}
+        \makeglossaries
 
-        \AtEndPreamble{\hypersetup{colorlinks=true,linkcolor=blue,urlcolor=blue,citecolor=red}}
     extra-dependencies:
       - float
       - multicol
 
 bibliography: references.bib
 link-citations: true
+colorlinks: true
+linkcolor: purple
+urlcolor: blue
+citecolor: red
 editor-options:
   markdown:
     wrap: 72
@@ -33,7 +39,16 @@ editor-options:
 
 ## Paper one [@Shin_2014]
 
-## Paper two [@Suhre_2011]
+\newglossaryentry{mr}{
+	name={Mendelian randomization},
+	description={Using genetic variants as instruments to infer causal effects}
+}
+
+\newacronym{gdm}{GDM}{Genetically Determined Metabotype}
+
+Here is an example of learning new vocabilary such as \gls{mr} and defining it in the glossary.
+
+## Short title of paper [@Suhre_2011]
 
 # Topic two
 
@@ -41,11 +56,12 @@ editor-options:
 
 <!-- Add youtube channels and databse links here -->
 # Online resources
+- [Human Metabolome Database](https://www.hmdb.ca/)
 
 \newpage
 
-<!-- For listing and defining new vocabulary -->
-# Glossary
+<!-- For listing and defining new vocabulary, done automatically -->
+\printglossaries
 
 \newpage
 
-- 
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