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
@@ -1,31 +1,30 @@
 <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+request of the data provider and is no longer updated or displayed.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.
 <H2>Display conventions</H2>
 </p><p>
 By default, each variant is labeled with the nucleotide change. Hover over the
 feature to see more information, explained on the track details page of the particular track
 or when clicking onto the feature.  </p>
 <H2>Credits</H2>
 <p>
 For data provenance, access and descriptions, please click the documentation via the link above.
 </p>