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/mouse/refSeqComposite.mm10.mm39.ra src/hg/makeDb/trackDb/mouse/refSeqComposite.mm10.mm39.ra
index 09b02ab76c8..b9b7421f06d 100644
--- src/hg/makeDb/trackDb/mouse/refSeqComposite.mm10.mm39.ra
+++ src/hg/makeDb/trackDb/mouse/refSeqComposite.mm10.mm39.ra
@@ -1,29 +1,29 @@
 track refSeqComposite
 compositeTrack on
 shortLabel NCBI RefSeq
 longLabel RefSeq genes from NCBI
 group genes
 visibility dense
 type genePred
 dragAndDrop subTracks
 noInherit on
 #subGroup1 view Views aNcbiRefSeq=NCBI_RefSeq zUcscRefSeq=UCSC_RefSeq
 allButtonPair on
 dataVersion /gbdb/$D/ncbiRefSeq/ncbiRefSeqVersion.txt
 priority 2
-dbPrefixUrls hg="http://www.genenames.org/cgi-bin/gene_symbol_report?hgnc_id=$$" dm="http://flybase.org/reports/$$" ce="http://www.wormbase.org/db/gene/gene?name=$$" rn="https://rgd.mcw.edu/rgdweb/search/search.html?term=$$" sacCer="https://www.yeastgenome.org/locus/$$" danRer="https://zfin.org/$$" mm="https://www.informatics.jax.org//marker/$$" xenTro="https://www.xenbase.org/gene/showgene.do?method=display&geneId=$$"
+dbPrefixUrls hg="http://www.genenames.org/cgi-bin/gene_symbol_report?hgnc_id=$$" dm="https://flybase.org/reports/$$" ce="http://www.wormbase.org/db/gene/gene?name=$$" rn="https://rgd.mcw.edu/rgdweb/search/search.html?term=$$" sacCer="https://www.yeastgenome.org/locus/$$" danRer="https://zfin.org/$$" mm="https://www.informatics.jax.org//marker/$$" xenTro="https://www.xenbase.org/gene/showgene.do?method=display&geneId=$$"
 dbPrefixLabels hg="HGNC" dm="FlyBase" ce="WormBase" rn="RGD" sacCer="SGD" danRer="ZFIN" mm="MGI" xenTro="XenBase"
 
         track ncbiRefSeq
         parent refSeqComposite off
         color 12,12,120
         shortLabel RefSeq All
         longLabel NCBI RefSeq genes, curated and predicted (NM_*, XM_*, NR_*, XR_*, NP_*, YP_*)
         idXref ncbiRefSeqLink mrnaAcc name
         baseColorUseCds given
         baseColorDefault genomicCodons
         priority 1
 
         track ncbiRefSeqCurated
         color 12,12,120
         parent refSeqComposite on
@@ -44,31 +44,31 @@
         baseColorDefault genomicCodons
         priority 3
 
         track ncbiRefSeqOther
         color 32,32,32
         parent refSeqComposite off
         shortLabel RefSeq Other
         longLabel NCBI RefSeq Other Annotations (not NM_*, NR_*, XM_*, XR_*, NP_* or YP_*)
         priority 4
         searchIndex name
         searchTrix /gbdb/$D/ncbiRefSeq/ncbiRefSeqOther.ix
         bigDataUrl /gbdb/$D/ncbiRefSeq/ncbiRefSeqOther.bb
         type bigBed 12 +
         labelFields gene
         skipEmptyFields on
-        urls GeneID="https://www.ncbi.nlm.nih.gov/gene/$$" MIM="https://www.ncbi.nlm.nih.gov/omim/612091" HGNC="https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/$$" FlyBase="http://flybase.org/reports/$$" WormBase="http://www.wormbase.org/db/gene/gene?name=$$" RGD="https://rgd.mcw.edu/rgdweb/search/search.html?term=$$" SGD="https://www.yeastgenome.org/locus/$$" miRBase="http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=$$" ZFIN="https://zfin.org/$$" MGI="https://www.informatics.jax.org//marker/$$"
+        urls GeneID="https://www.ncbi.nlm.nih.gov/gene/$$" MIM="https://www.ncbi.nlm.nih.gov/omim/612091" HGNC="https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/$$" FlyBase="https://flybase.org/reports/$$" WormBase="http://www.wormbase.org/db/gene/gene?name=$$" RGD="https://rgd.mcw.edu/rgdweb/search/search.html?term=$$" SGD="https://www.yeastgenome.org/locus/$$" miRBase="http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=$$" ZFIN="https://zfin.org/$$" MGI="https://www.informatics.jax.org//marker/$$"
 
         track ncbiRefSeqPsl
         priority 5
         parent refSeqComposite off
         shortLabel RefSeq Alignments
         longLabel RefSeq Alignments of RNAs
         type psl
         indelDoubleInsert on
         indelQueryInsert on
         showDiffBasesAllScales .
         showDiffBasesMaxZoom 10000.0
         showCdsMaxZoom 10000.0
         showCdsAllScales .
         baseColorDefault diffCodons
         pslSequence no