902ddcd7fbb3d57866a542f85eecdaaf16f58684
gperez2
  Wed Nov 5 12:31:44 2025 -0800
Edits to the Varaico update, refs #36612

diff --git src/hg/makeDb/trackDb/human/varaico.html src/hg/makeDb/trackDb/human/varaico.html
index 891d977ed72..4fd6b2fc276 100755
--- src/hg/makeDb/trackDb/human/varaico.html
+++ src/hg/makeDb/trackDb/human/varaico.html
@@ -1,106 +1,110 @@
 <H2>Description</H2>
 <div class="warn-note" style="border: 2px solid #c70039; padding: 5px 20px; background-color: #fadbd8;">
 <p><span style="font-weight: bold; color: #c70000;">NOTE:</span><br>
 Some rights reserved. This work permits non-commercial use, distribution and reproduction in any
 medium, provided the original author and source are credited.
 <br>
 License and legal information can be found on the <a href="https://varaico.com/license"
 target="_blank">Varaico website</a>.</p>
 </div>
 
 <p>
 <a href="https://varaico.com/" target="_blank">Varaico</a>
 (<b>Va</b>riation <b>R</b>esearch <b>A</b>dvancing <b>I</b>nsight in <b>C</b>omplex
 <b>O</b>rganisms) was created using
 literature mining, similar to AVADA. Varaico variants are generated by an automated process that
 extracts purely factual information about genes from scientific papers (by matching strings against
 gene names) and HGVS variant descriptions (using regular expressions). Varaico aims to reduce
 false-positive gene and variant mentions and link them together appropriately, but nonetheless, many
 variants displayed are not mapped to the genomic position intended by the authors.
 </p>
 
 <p><b>Varaico Variants (suppl)</b> contains variants extracted from supplementary data files
 using similar methods as in the Varaico track.</p>
 
 <p>
 For data questions, Varaico can be contacted at
 <A HREF="mailto:&#106;&#98;&#105;&#114;&#103;m&#101;i&#64;&#103;&#109;&#97;i&#108;.
 &#99;&#111;&#109;">
 &#106;&#98;&#105;&#114;&#103;m&#101;i&#64;&#103;&#109;&#97;i&#108;.&#99;&#111;&#109;</A>
 <!-- above address is jbirgmei at gmail.com -->
 </p>
 
 <h2>Display Conventions and Configuration</h2>
 
 <p>
 Genomic locations of variants are labeled with the HGNC gene symbol and the variant change.
 Mouse over the variants to show the gene, variant, latest author/year/title, number of publications
 mentioning the variant, and variant effect.</p>
 
 <p>
 Clicking on an item will provide a link directly to
 Varaico to view all publications mentioning this variant.</p>
 
 <p>
 The items are colored based on the amount of literature support and are a gradient from the
 colors described on the table below:
 </p>
 
 <p>
 <table>
   <thead>
   <tr>
     <th style="border-bottom: 2px solid #6678B1;">Color</th>
     <th style="border-bottom: 2px solid #6678B1;">Level of literature support</th>
   </tr>
   </thead>
   <tr>
     <th bgcolor="#3B4DC1"></th>
     <th align="left">&gt;20 papers mention the variant</th>
   </tr>
   <tr>
     <th bgcolor="#B30326"></th>
     <th align="left">&nbsp;&nbsp;20 papers mention the variant</th>
   </tr>
   <tr>
     <th bgcolor="#F59E7F"></th>
     <th align="left">&nbsp;&nbsp;15 papers mention the variant</th>
   </tr>
   <tr>
     <th bgcolor="#D6DBE4"></th>
     <th align="left">&nbsp;&nbsp;10 papers mention the variant</th>
   </tr>
   <tr>
     <th bgcolor="#7EA1F9"></th>
     <th align="left">&nbsp;&nbsp;&nbsp;&nbsp;5 papers mention the variant</th>
   </tr>
   <tr>
     <th bgcolor="#3A4CC0"></th>
     <th align="left">&nbsp;&nbsp;&nbsp;&nbsp;1 paper mentions the variant</th>
   </tr>
 </table>
 </p>
 
 
 <H2>Data access</H2>
 <p>
 The raw data can be explored interactively with the <a href="../cgi-bin/hgTables">Table Browser</a>
 or the <a href="../cgi-bin/hgIntegrator">Data Integrator</a>. The data can be accessed from scripts through our
 <a href="https://api.genome.ucsc.edu">API</a>, the track name is &quot;varaico&quot;. </p>
 
 <p>
 For automated download and analysis, the genome annotation is stored in a bigBed file that
 can be downloaded from
 <a href="http://hgdownload.soe.ucsc.edu/gbdb/$db/bbi/" target="_blank">our download server</a>.
 The file for this track is called <tt>varaico.bb</tt>. Individual
-regions or the whole genome annotation can be obtained using our tool <tt>bigBedToBed</tt>
+regions or the whole genome annotation can be obtained using our tool <tt>bigBedToBed</tt>,
 which can be compiled from the source code or downloaded as a precompiled
 binary for your system. </p>
 <p>
+The previous Varaico Variants version is also available in our
+<a href="https://hgdownload.soe.ucsc.edu/goldenPath/archive/$db/varaico/"
+target="_blank">download archive</a>.</p>
+<p>
 Instructions for downloading source code and binaries can be found
 <a href="http://hgdownload.soe.ucsc.edu/downloads.html#utilities_downloads">here</a>.
 The tool
 can also be used to obtain only features within a given range, e.g.
 <br><br>
 <tt>bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/hg38/bbi/varaico.bb -chrom=chr21 -start=0 -end=10000000 stdout</tt></p>
 </p>