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/ikmc.html src/hg/makeDb/trackDb/mouse/ikmc.html
index af8d3c6f95d..945778c4c59 100644
--- src/hg/makeDb/trackDb/mouse/ikmc.html
+++ src/hg/makeDb/trackDb/mouse/ikmc.html
@@ -1,123 +1,123 @@
 <H3>Description</H3>
 <P>
 This track shows genes targeted by 
 <A HREF="https://www.mousephenotype.org/martsearch_ikmc_project/about"
 TARGET=_BLANK>International Knockout Mouse Consortium (IKMC)</A>, a 
 collaboration to generate a public resource of mouse embryonic stem (ES)
 cells containing a null mutation in every gene in the mouse genome.
 Gene targets are color-coded by status:
 <UL>
 <LI><span style="color: #00F000; font-weight: bold;">Green</span>: Reagent(s) Available</LI>
 <LI><span style="color: #FFD000; font-weight: bold;">Yellow</span>: In Progress</LI>
 <LI><span style="color: #0000C8; font-weight: bold;">Blue</span>: Not Started/On Hold</LI>
 <LI><span style="color: #000; font-weight: bold;">Black</span>: Withdrawn/Problematic</LI>
 </UL>
 </P>
 <P>
 The <A HREF="https://www.mousephenotype.org/martsearch_ikmc_project/aboutkompdcc" TARGET=_BLANK>KnockOut Mouse Project Data
 Coordination Center (KOMP DCC)</A> is the central database resource
 for coordinating mouse gene targeting within IKMC and provides
 web-based query and display tools for IKMC data.  In addition, the
 KOMP DCC website provides a tool for the scientific community to
 nominate genes of interest to be knocked out by the KOMP initiative.</P>
 
 <P>
 IKMC members include
 <UL>
 <LI><a href="https://www.mousephenotype.org/martsearch_ikmc_project/aboutkomp" TARGET=_BLANK>KnockOut
     Mouse Project (KOMP)</a>, a trans-NIH initiative (USA)</LI>
 <LI><a href="https://www.mousephenotype.org/about-impc/about-ikmc/eucomm/" TARGET=_BLANK>European
     Conditional Mouse Mutagenesis Program (EUCOMM)</a>, funded by the
     European Union Framework 6 programme (EU)</LI>
 <LI><a href="http://norcomm.org/index.htm"
     TARGET=_BLANK>North American Conditional Mouse Mutagenesis Project
     (NorCOMM)</a>, a Genome Prairie Project (Canada)</LI>
 <LI><a href="https://www.tigm.org/" TARGET=_BLANK>Texas A&amp;M
     Institute for Genomic Medicine (TIGM)</a> (USA)</LI>
 </UL>
 
 KOMP includes two production centers: 
-CSD, a collaborative team at the <A HREF="http://www.chori.org/drupal1/"
+CSD, a collaborative team at the <A HREF="https://bacpacresources.org/"
 TARGET=_BLANK>Children's Hospital Oakland Research Institute
 (CHORI)</A>, the <A HREF="https://www.sanger.ac.uk/research/projects/genetrap/"
 TARGET=_BLANK>Wellcome Trust Sanger Institute</A> and the University
 of California at Davis <A HREF="https://www.vetmed.ucdavis.edu/"
 TARGET=_BLANK>School of Veterinary Medicine</A>, and 
 a team at the <A HREF="https://www.regeneron.com/technology"
 TARGET=_BLANK>VelociGene</A> division of Regeneron Pharmaceuticals, Inc.
 EUCOMM includes <A HREF="https://www.mousephenotype.org/about-impc/about-ikmc/eucomm/"
 TARGET=_BLANK>9 participating institutions</A>.  
 NorCOMM includes several <A HREF="http://norcomm.org/research_partners.htm" 
 TARGET=_BLANK>participating institutions</A>.
 </P>
 <P>
 Items displayed as a solid box represent the gene regions targeted by
 the Regeneron gene knockout strategy.  In most cases Regeneron alleles
 will be complete null alleles that delete the entire protein coding
 sequence of the target gene.</P>
 <P>
 Items displayed as lines connecting short boxes represent the
 targeting vector construct strategy used by EuCOMM, NorCOMM, and
 CSD. This strategy relies on the identification of a
 &quot;critical&quot; exon common to all transcript variants that, when
 deleted, creates a frame-shift mutation.  The short boxes in the middle 
 of an item show the vector features that surround the critical exon.
 </P>
 
 <H3>Methods</H3>
 <P>
 Using <A HREF="https://www.mousephenotype.org/martsearch_ikmc_project/aboutkompstrategies"
 TARGET=_BLANK>complementary targeting strategies</A>, the IKMC centers 
 design and create targeting vectors, mutant ES cell lines and, to some
 extent, mutant mice, embryos or sperm. Materials are distributed to
 the research community.</P>
 <P>
 The <A HREF="https://www.komp.org/index.php?link=5" TARGET=_BLANK>KOMP Repository</A> 
 archives, maintains, and distributes IKMC products. Researchers can
 order products and get product information from the
 Repository. Researchers can also express interest in products that are
 still in the pipeline. They will then receive email notification as
 soon as KOMP generated products are available for distribution.</P>
 <P>
 The process for ordering EUCOMM materials can be found 
 <A HREF="https://www.mousephenotype.org/martsearch_ikmc_project/about/eucomm" TARGET=_BLANK>here</A>.</P>
 <P>
 The process for ordering TIGM materials can be found 
 <A HREF="https://www.tigm.org/repository/" TARGET=_BLANK>here</A>.</P>
 <P>
 Information on NorCOMM products and services can be found 
 <A HREF="http://norcomm.org/accessing_services.htm"
 TARGET=_BLANK>here</A>.</P>
 
 <H3>Credits</H3>
 <P>
 Thanks to the <A HREF="https://www.mousephenotype.org/martsearch_ikmc_project/about"
 TARGET=_BLANK>International Knockout Mouse Consortium</A>, and Carol Bult in 
 particular, for providing these data.</P>
 
 <H3>References</H3>
 <p>
 Austin CP, Battey JF, Bradley A, Bucan M, Capecchi M, Collins FS, Dove WF, Duyk G, Dymecki S, Eppig
 JT <em>et al</em>.
 <a href="https://www.nature.com/articles/ng0904-921" target="_blank">
 The knockout mouse project</a>.
 <em>Nat Genet</em>. 2004 Sep;36(9):921-4.
 PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/15340423" target="_blank">15340423</a>; PMC: <a
 href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2716027/" target="_blank">PMC2716027</a>
 </p>
 
 <p>
 Collins FS, Finnell RH, Rossant J, Wurst W.
 <a href="https://www.sciencedirect.com/science/article/pii/S0092867407004643" target="_blank">
 A new partner for the international knockout mouse consortium</a>.
 <em>Cell</em>. 2007 Apr 20;129(2):235.
 PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/17448981" target="_blank">17448981</a>
 </p>
 
 <p>
 International Mouse Knockout Consortium, Collins FS, Rossant J, Wurst W.
 <a href="https://www.sciencedirect.com/science/article/pii/S0092867406016126" target="_blank">
 A mouse for all reasons</a>.
 <em>Cell</em>. 2007 Jan 12;128(1):9-13.
 PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/17218247" target="_blank">17218247</a>
 </p>