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/hgIkmc.html src/hg/makeDb/trackDb/human/hgIkmc.html index 43a4d8c04a0..b479b824575 100644 --- src/hg/makeDb/trackDb/human/hgIkmc.html +++ src/hg/makeDb/trackDb/human/hgIkmc.html @@ -1,116 +1,115 @@ <H3>Description</H3> <P> This track shows genes targeted by <a href="https://www.mousephenotype.org/about-impc/about-ikmc/" target="_blank">International Knockout Mouse Consortium (IKMC)</a> mapped to the human genome. IKMC is 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: Withdrawn/Problematic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/about-impc/about-komp/" 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/about-impc/about-komp/" 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="https://www.umanitoba.ca/institutes/manitoba_institute_cell_biology/norcomm/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&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="http://www.sanger.ac.uk/science/collaboration/sanger-institute-gene-trap- -resource" target="_blank">Wellcome Trust Sanger Institute</a> and the University +(CHORI)</A>, the <a href="https://www.sanger.ac.uk/collaboration/sanger-institute-gene-trap-resource/" 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="https://umanitoba.ca/institutes/manitoba_institute_cell_biology/norcomm/research_partners.htm" TARGET=_BLANK>participating institutions</A>. </P> <H3>Methods</H3> <P> Using <a href="https://www.mousephenotype.org/about-impc/targeting-strategies/" 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" 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/about-impc/about-ikmc/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="https://www.umanitoba.ca/institutes/manitoba_institute_cell_biology/norcomm/accessing_services.htm" TARGET=_BLANK>here</A>. </P><P> Genes were mapped to the human genome by IKMC. </P> <H3>Credits</H3> <P> Thanks to the <a href="https://www.mousephenotype.org/about-impc/about-ikmc/" 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>