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/orfeomeMrna.html src/hg/makeDb/trackDb/orfeomeMrna.html
index cfa8c89b307..b598083eb39 100644
--- src/hg/makeDb/trackDb/orfeomeMrna.html
+++ src/hg/makeDb/trackDb/orfeomeMrna.html
@@ -1,37 +1,35 @@
 <h2>Description</h2>
 
 <p>
 This track show alignments of $organism clones from the
-<a href="http://www.orfeomecollaboration.org/" target="_blank">
-ORFeome Collaboration</a>.  The goal of the project is to be an
+ORFeome Collaboration.  The goal of the project is to be an
 &quot;unrestricted source of fully sequence-validated full-ORF human cDNA
 clones in a format allowing easy transfer of the ORF sequences into
 virtually any type of expression vector.  A major goal is to provide
 at least one fully-sequenced full-ORF clone for each human, mouse, and zebrafish gene.
 This track is updated automatically as new clones become available.
 </p>
 
 <h2>Display Conventions and Configuration</h2>
 
 <p>
 The track follows the display conventions for
 <a href="../goldenPath/help/hgTracksHelp.html#GeneDisplay">gene prediction
 tracks</a>.</p>
 
 <h2>Methods</h2>
 
 <p>
 ORFeome $organism clones were obtained from GenBank and aligned against the
 genome using the blat program. When a single clone aligned in multiple
 places, the alignment having the highest base identity was found.  Only alignments
 having a base identity level within 0.5% of the best and at least 96% base
 identity with the genomic sequence were kept.
 </p>
 
 <h2>Credits and References</h2>
 
 <p>
 Visit the ORFeome Collaboration
-<a href="http://www.orfeomecollaboration.org/?pageID=32" target="_blank">
-members page</a> for a list of credits and references.
+members page for a list of credits and references.
 </p>