089c09e98db52e92da694ab1a0c8891c1a7fd3e8
gperez2
  Thu Apr 2 15:50:07 2026 -0700
Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run).

Updated 261 trackDb HTML and .ra files:
- Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs,
chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations;
removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download,
oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs).
- Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com,
drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains
(blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix);
removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com).
- Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org,
cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org,
hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path).

No RM.

diff --git src/hg/makeDb/trackDb/ensGene.html src/hg/makeDb/trackDb/ensGene.html
index c234ad2c0c9..7677f8237d5 100644
--- src/hg/makeDb/trackDb/ensGene.html
+++ src/hg/makeDb/trackDb/ensGene.html
@@ -1,59 +1,59 @@
 <h2>Description</h2>
 
 <p>
-These gene predictions were generated by <a href="http://www.ensembl.org/index.html"
+These gene predictions were generated by <a href="https://www.ensembl.org/index.html"
 target="_blank">Ensembl</a>.
 </p>
 
 <p>
 For more information on the different gene tracks, see our <a target=_blank 
 href="/FAQ/FAQgenes.html">Genes FAQ</a>.</p>
 
 <h2>Methods</h2>
 
 <p>
 For a description of the methods used in Ensembl gene predictions, please refer to
 <a href="https://academic.oup.com/nar/article/30/1/38/1332872/The-Ensembl-genome-database-project"
 target="_blank">Hubbard <em>et al</em>. (2002)</a>, also listed in the References section below. 
 </p>
 
 <h2>Data access</h2>
 <p>
 Ensembl Gene data can be explored interactively using the
 <a href="/cgi-bin/hgTables" target="_blank">Table Browser</a> or the
 <a href="/cgi-bin/hgIntegrator" target="_blank">Data Integrator</a>. 
 For local downloads, the genePred format files for $db are available in our
 <a target="_blank" href="http://hgdownload.soe.ucsc.edu/goldenPath/$db/database/">
 downloads directory</a> as ensGene.txt.gz or in our
 <a target="_blank" href="http://hgdownload.soe.ucsc.edu/goldenPath/$db/bigZips/genes">
 genes download directory</a> in GTF format.<br><br>
 For programmatic access, the data can be queried from the 
 <a href="../goldenPath/help/api.html" target="_blank">REST API</a> or
 directly from our public MySQL
 servers. Instructions on this method are available on our
 <a target="_blank" href="/goldenPath/help/mysql.html">MySQL help page</a> and on
 <a target="_blank" href="http://genome.ucsc.edu/blog/tag/mysql/">our blog</a>.</p>
 
 <p>
 Previous versions of this track can be found on our <a href="http://hgdownload.soe.ucsc.edu/goldenPath/archive/$db/ensGene">archive download server</a>.
 </p>
 
 <h2>Credits</h2>
 
 <p>
 We would like to thank Ensembl for providing these gene annotations. For more information, please see
-<a href="https://uswest.ensembl.org/info/genome/genebuild/index.html"
+<a href="https://www.ensembl.org/info/genome/genebuild/index.html"
 target=_blank>Ensembl&#39s genome annotation page.</a>
 </p> 
 
 <h2>References</h2>
 
 <p>
 Hubbard T, Barker D, Birney E, Cameron G, Chen Y, Clark L, Cox T, Cuff J,
 Curwen V, Down T <em>et al</em>.
 <a href="https://academic.oup.com/nar/article/30/1/38/1332872/The-Ensembl-genome-database-project"
 target="_blank">The Ensembl genome database project</a>.
 <em>Nucleic Acids Res</em>. 2002 Jan 1;30(1):38-41.
 PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/11752248" target="_blank">11752248</a>; PMC: <a
 href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC99161/" target="_blank">PMC99161</a>
 </p>