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/trackDb.ra src/hg/makeDb/trackDb/trackDb.ra
index 066c3808345..3ed9dd2b761 100644
--- src/hg/makeDb/trackDb/trackDb.ra
+++ src/hg/makeDb/trackDb/trackDb.ra
@@ -534,31 +534,31 @@
 shortLabel Ensembl Genes
 longLabel Ensembl Genes
 group genes
 exonNumbers on
 visibility hide
 color 150,0,0
 type genePred ensPep
 
 track ensEstGene
 shortLabel Ensembl EST Genes
 longLabel Ensembl EST Gene Predictions
 group genes
 visibility hide
 color 150,0,0
 type genePred ensEstPep
-url http://www.ensembl.org/perl/geneview?db=estgene&transcript=$$
+url https://www.ensembl.org/perl/geneview?db=estgene&transcript=$$
 
 track sibGene
 shortLabel SIB Genes
 longLabel Swiss Institute of Bioinformatics Gene Predictions from mRNA and ESTs
 group  genes
 visibility hide
 color 195,90,0
 type genePred
 url http://ccg.vital-it.ch/cgi-bin/tromer/tromer_quick_search_internal.pl?query_str=$$
 urlLabel SIB link:
 
 track ECgene
 shortLabel ECgene Genes
 longLabel ECgene Gene Predictions with Alt-Splicing
 group genes