From e69b687cbc938520faab65f1cd92b9da4b74827f Mon Sep 17 00:00:00 2001
From: hoytpr <peter.r.hoyt@okstate.edu>
Date: Thu, 28 Mar 2019 10:17:09 -0500
Subject: [PATCH] Adding glossary to replace FIXME

---
 reference.md | 68 ++++++++++++++++++++++++++++++++++++++++++++++++++--
 1 file changed, 66 insertions(+), 2 deletions(-)

diff --git a/reference.md b/reference.md
index 6260be63..72396270 100644
--- a/reference.md
+++ b/reference.md
@@ -1,8 +1,72 @@
 ---
 layout: reference
-title: Reference
 ---
 
 ## Glossary
 
-FIXME
+{:auto_ids}  
+accession
+:   a unique identifier assigned to each sequence or set of sequences
+
+BLAST
+:   The Basic Local Alignment Search Tool at NCBI that searches for similarities between known and unknown biomolecules like DNA
+
+categorical variable
+:   Variables can be classified as categorical (aka, qualitative) or quantitative (aka, numerical). Categorical variables take on a fixed number of values that are names or labels. 
+
+cleaned data  
+:   data that has been manipulated post-collection to remove errors or inaccuracies, introduce desired formatting changes, or otherwise prepare the data for analysis
+
+conditional formatting  
+:   formatting that is applied to a specific cell or range of cells depending on a set of criteria  
+
+CSV (comma separated values) format  
+:   a plain text file format in which values are separated by commas
+
+factor  
+:   a variable that takes on a limited number of possible values (i.e. categorical data)
+
+Gb
+:   gigabyte of file storage or file size
+
+Gbase
+:   a gigabase represents one billion nucleic acid bases (Gbp may indicate one billion base pairs of nucleic acid)
+
+headers
+:   names at tops of columns that are descriptive about the column contents (sometimes optional)
+
+metadata  
+:   data which describes other data  
+
+NGS
+:   common acronym for "Next Generation Sequencing" currently being replaced by "High Throughput Sequencing"
+
+null value  
+:   a value used to record observations missing from a dataset
+
+observation  
+:   a single measurement or record of the object being recorded (e.g. the weight of a particular mouse)
+
+plain text
+:   unformatted text
+
+quality assurance  
+:   any process which checks data for validity during entry  
+
+quality control  
+:   any process which removes problematic data from a dataset
+
+raw data  
+:   data that has not been manipulated and represents actual recorded values
+
+rich text  
+:  formatted text (e.g. text that appears bolded, colored or italicized)
+
+string  
+:   a collection of characters (e.g. "thisisastring")
+
+TSV (tab separated values) format  
+:   a plain text file format in which values are separated by tabs
+
+variable  
+:   a category of data being collected on the object being recorded (e.g. a mouse's weight)
\ No newline at end of file