fa29b7e72d8fb2a9519bf14f1122feccfd79eca2
lrnassar
  Thu Jun 11 04:46:21 2026 -0700
Retire mastermind track by gating it to alpha and noting retirement on the varsInPubs description page. refs #37753

The Genomenon Mastermind track no longer updates and the provider asked us to
take it down. Added release alpha to the mastermind subtrack so it stays on
dev/sandbox but is removed from beta and public for both hg38 and hg19, and
updated the varsInPubs.html bullet to note the track has been retired.

diff --git src/hg/makeDb/trackDb/human/varsInPubs.html src/hg/makeDb/trackDb/human/varsInPubs.html
index e834f0301eb..3f51d9ed10b 100644
--- src/hg/makeDb/trackDb/human/varsInPubs.html
+++ src/hg/makeDb/trackDb/human/varsInPubs.html
@@ -1,22 +1,21 @@
 <H2>Description</H2>
 <p>The tracks that are listed here contain genetic variants and links to scientific publications that 
 mention them.</p>
 <ul>
-<li>The <b>Mastermind</b> track was created by Genomenon, a company that analyzes fulltext 
-of publications with their own proprietary software with an unknown false
-positive rate.</li>
+<li>The <b>Mastermind</b> track, created by Genomenon, has been retired at the
+request of the data provider and is no longer updated or displayed.</li>
 <li>The <b><a target="_blank" href="https://varchat.engenome.com/">VarChat</a></b> 
 track was created by enGenome and links to its proprietary 
 software, VarChat, with an unknown false positive rate.</li>
 <li>The <b>AVADA</b> track was created in the Bejerano lab at
 Stanford by J. Birgmeier also on fulltext papers, using sophisticated machine learning
 methods and was evaluated to have a false positive rate of around 50% in their study.</li>
 <li>The <b>PubTator rsIDs</b> track was created using 
 <a href="https://ftp.ncbi.nlm.nih.gov/pub/lu/PubTator3/">PubTator 3 data</a>.</li>
 <li>The <b>Varaico</b> tracks were created using literature mining in a fashion similar to AVADA. Coloring
 is a gradient between blue and red, and represent the number of publications per variant. See
 the <a href="https://varaico.com/">Varaico website</a> for more details.</li>
 </ul>
 
 </p><p>
 For additional information please click on the hyperlink of the respective track above.