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/human/trackDb.ra src/hg/makeDb/trackDb/human/trackDb.ra
index 8ab19b51f51..128f79f0d88 100644
--- src/hg/makeDb/trackDb/human/trackDb.ra
+++ src/hg/makeDb/trackDb/human/trackDb.ra
@@ -3294,53 +3294,53 @@
 #url2 http://microrna.sanger.ac.uk/cgi-bin/sequences/mirna_entry.pl?id=$$
 url2 http://www.mirbase.org/cgi-bin/query.pl?terms=$$
 dataVersion miRBase Release 13.0 (March 2009) and snoRNABase Version 3
 
 track lrgTranscriptAli
 shortLabel LRG Transcripts
 longLabel Locus Reference Genomic (LRG) / RefSeqGene Fixed Transcript Annotations
 group genes
 visibility hide
 type bigPsl
 html lrgTranscriptAli
 #mouseOver ${name}: ${ncbiTranscript} ${ensemblTranscript} ${ncbiProtein} ${ensemblProtein} ${geneName}
 skipFields mouseOver
 exonNumbers on
 skipEmptyFields on
-urls ncbiTranscript=https://www.ncbi.nlm.nih.gov/nuccore/$$ ensemblTranscript=http://www.ensembl.org/Multi/Search/Results?site=ensembl_all;q=$$ ncbiProtein=https://www.ncbi.nlm.nih.gov/protein/$$ ensemblProtein=http://www.ensembl.org/Multi/Search/Results?site=ensembl_all;q=$$
+urls ncbiTranscript=https://www.ncbi.nlm.nih.gov/nuccore/$$ ensemblTranscript=https://www.ensembl.org/Multi/Search/Results?site=ensembl_all;q=$$ ncbiProtein=https://www.ncbi.nlm.nih.gov/protein/$$ ensemblProtein=https://www.ensembl.org/Multi/Search/Results?site=ensembl_all;q=$$
 altColor 127,127,127
 baseColorDefault genomicCodons
 baseColorUseSequence lfExtra
 indelDoubleInsert on
 indelPolyA on
 indelQueryInsert on
 showDiffBasesAllScales .
 showDiffBasesMaxZoom 10000.0
 showCdsAllScales .
 showCdsMaxZoom 10000.0
 color 54,125,29
 urlLabel Link to LRG transcript
 url http://ftp.ebi.ac.uk/pub/databases/lrgex/$<_lrgParent>.xml#transcripts_anchor
 bigDataUrl /gbdb/$D/bbi/lrgBigPsl.bb
 searchIndex name
 
 track affyHuEx1
 shortLabel Affy HuEx 1.0
 longLabel Affymetrix Human Exon 1.0 Probe Sets
 group expression
 visibility hide
-url http://www.affymetrix.com/analysis/netaffx/exon/probe_set.affx?pk=1:$$
+url https://www.affymetrix.com/analysis/netaffx/exon/probe_set.affx?pk=1:$$
 urlLabel Netaffx Link:
 useScore 1
 type bed 6 .
 
 track affyHumanExon
 shortLabel Affy All Exon
 longLabel Affymetrix All Exon Chips
 group expression
 visibility hide
 type expRatio
 expScale 4.0
 expStep 0.5
 expProbeTable affyHumanExonProbeAnnot
 expTable affyHumanExonExps
 groupings affyHumanExonGroups