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/ensemblGeneScaffold.html src/hg/makeDb/trackDb/ensemblGeneScaffold.html
index 51a2f0765f9..5eb07d81b64 100644
--- src/hg/makeDb/trackDb/ensemblGeneScaffold.html
+++ src/hg/makeDb/trackDb/ensemblGeneScaffold.html
@@ -1,43 +1,43 @@
 <h2>Description</h2>
 
 <p>
 This track shows the mapping of Ensembl gene scaffold coordinates onto
 the underlying assembly contigs or scaffolds.  Items are displayed in black
 and gray.  Gray items indicate segments of the gene scaffold that do not map
 in linear order to the underlying contig or scaffold.
 </p>
 
 <p>
 These gene scaffolds were generated by
-<a href="http://www.ensembl.org/index.html" target="_blank">Ensembl</a>.
+<a href="https://www.ensembl.org/index.html" target="_blank">Ensembl</a>.
 </p>
 
 <h2>Methods</h2>
 
 <p>
 This track is created from the Ensembl MySQL tables: <em>assembly.txt</em>
 and <em>seq_region.txt</em>.
 </p>
 
 <p>
 For a description of the methods used in Ensembl gene prediction, refer to
 Hubbard <em>et al</em>. (2002) in the References section below.
 </p>
 
 <h2>Credits</h2>
 
 <p>
 Thanks to Ensembl for providing this annotation.
 </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>