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/rikenCageTc.html src/hg/makeDb/trackDb/mouse/rikenCageTc.html
index d8c8491da73..4e1edf06f60 100644
--- src/hg/makeDb/trackDb/mouse/rikenCageTc.html
+++ src/hg/makeDb/trackDb/mouse/rikenCageTc.html
@@ -16,44 +16,44 @@
 <H2>Methods</H2>
 <P>
 The CAGE tags are sequenced from the 5' ends of full-length cDNAs produced using 
 RIKEN full-length cDNA technology. 
 
 To create the tag, a linker was 
 attached to the 5' end of full-length cDNAs which had been selected by cap 
 trapping. The first 20 bp of the cDNA were cleaved using the class II 
 restriction enzyme, MmeI, followed by PCR amplification. Concatamers
 of the resulting 32 bp tags were then formed for more efficient sequencing. 
 
 For more information on 
 CAGE, see Shiraki <em>et al.</em> (2003) and Carninci <EM>et al</EM> (2005). 
 
 
-<A HREF="http://genome.gsc.riken.go.jp/home.html" TARGET=_blank>RIKEN</A> 
+<A HREF="https://www.riken.jp/en/" TARGET=_blank>RIKEN</A> 
 website
 for information about RIKEN full-length cDNA technologies. 
 
 The mapping 
 methodology employed in this annotation will be described in upcoming 
 publications.</P>
 
 <H2>Credits</H2>
 <P>
 These data were contributed by the Functional Annotation of Mouse
 (<A HREF="https://fantom.gsc.riken.jp/" TARGET=_blank>FANTOM</A>)
 Consortium, RIKEN Genome Science Laboratory and
-<A HREF="http://genome.gsc.riken.jp/home.html" 
+<A HREF="https://www.riken.jp/en/" 
 TARGET=_blank> RIKEN Genome Exploration Research Group</A>
 (Genome Network Project Core Group).  </P>
 
 
 
 
 <P>
 <B>FANTOM Consortium:</B> P. Carninci, T. Kasukawa, S. Katayama, Gough, 
 M. Frith, N. Maeda, R. Oyama, T. Ravasi, B. Lenhard, C. Wells, R. 
 Kodzius, K. Shimokawa, V. B. Bajic, S. E. Brenner, S. Batalov, A. R. R. 
 Forrest, M. Zavolan, M. J. Davis, L. G. Wilming, V. Aidinis, J. Allen, 
 A. Ambesi-Impiombato, R. Apweiler, R. N. Aturaliya, T. L. Bailey, M. 
 Bansal, K. W. Beisel, T. Bersano, H. Bono,  A. M. Chalk, K. P. Chiu, V. 
 Choudhary, A. Christoffels, D. R. Clutterbuck, M. L. Crowe, E. Dalla, 
 B. P. Dalrymple, B. de Bono, G. Della Gatta, D. di Bernardo, T. Down,