55714b9d6370aa54873fe0c58e5618c984a357dc jnavarr5 Fri Nov 22 11:32:57 2019 -0800 Removing databases that do not exist anymore, refs #24408 diff --git src/hg/makeDb/trackDb/human/lovdComp.html src/hg/makeDb/trackDb/human/lovdComp.html index 1c5e8f6..79a8fec 100644 --- src/hg/makeDb/trackDb/human/lovdComp.html +++ src/hg/makeDb/trackDb/human/lovdComp.html @@ -37,72 +37,41 @@ Since Nov 2019, similar to the ClinVar track, the data is split into two subtracks, for variants with a length of <= 100bp and >100bp, respectively. </p> <p> LOVD is a flexible, freely-available tool for gene-centered collection and display of DNA variations. It is not a database itself, but rather a platform where curators store and analyze data. While the LOVD team and the biggest LOVD sites are run at the Leiden University Medical Center, LOVD installations and their curators are spread over the whole world. Most LOVD databases report at least some of their content back to Leiden to allow global cross-database search, which is, among others, exported to this UCSC Genome Browser track every month. </p> <p> A few LOVD databases are entirely missing from this track. Reasons include configuration issues and -intentionally blocked data search. During the last check in June 2015, the following databases did -not export any variants: +intentionally blocked data search. During the last check in November 2019, the following databases +did not export any variants: <ul> <li> <a href="http://www.ucl.ac.uk/ldlr/Current/" target="_blank">http://www.ucl.ac.uk/ldlr/Current/</a></li> <li> - <a href="http://brca.iarc.fr/LOVD/" target="_blank">http://brca.iarc.fr/LOVD/</a></li> + <a href="http://sysbio.org.cn/en/index.php" target="_blank">http://sysbio.org.cn/</a></li> <li> - <a href="http://bioinf4.fcm.unicamp.br/LOVD/" - target="_blank">http://bioinf4.fcm.unicamp.br/LOVD/</a></li> - <li> - <a href="http://vitigene.igib.res.in" target="_blank">http://vitigene.igib.res.in</a></li> - <li> - <a href="http://fishmap2.igib.res.in/mirlovd/" - target="_blank">http://fishmap2.igib.res.in/mirlovd/</a></li> - <li> - <a href="http://www.medgen.mcgill.ca/nndi/" - target="_blank">http://www.medgen.mcgill.ca/nndi/</a></li> - <li> - <a href="http://sysbio.org.cn/" target="_blank">http://sysbio.org.cn/</a></li> - <li> - <a href="http://genome.igib.res.in/PGx/" target="_blank">http://genome.igib.res.in/PGx/</a></li> - <li> - <a href="http://www-huge.uni-regensburg.de/BEST1_database/" - target="_blank">http://www-huge.uni-regensburg.de/BEST1_database/</a></li> - <li> - <a href="http://genome.igib.res.in/tblovd/" - target="_blank">http://genome.igib.res.in/tblovd/</a></li> - <li> - <a href="https://ab-openlab.csir.res.in/mitolsdb/" + <a href="https://ab-openlab.csir.res.in/mitolsdb/home.php" target="_blank">https://ab-openlab.csir.res.in/mitolsdb/</a></li> - <li> - <a href="http://genome.igib.res.in/snolovd/" - target="_blank">http://genome.igib.res.in/snolovd/</a></li> - <li> - <a href="http://www.genomed.org/lovd2/" target="_blank">http://www.genomed.org/lovd2/</a></li> - <li> - <a href="http://skingenetics.igib.res.in/" - target="_blank">http://skingenetics.igib.res.in/</a></li> - <li> - <a href="http://mitodyn.org/" target="_blank">http://mitodyn.org/</a></li> </ul> Curators who want to share data in their database so it is present in this track can find more details in the <a href="http://www.lovd.nl/3.0/faq#FAQ18" target="_blank">LOVD FAQ</a>.</p> <h2>Batch queries</h2> <p>The LOVD data is not available for download or for batch queries in the Table Browser. However, it is available for programmatic access via the <a href="https://ga4gh.org/#/beacon">Global Alliance Beacon API</a>, a web service that accepts queries in the form (genome, chromosome, position, allele) and returns "true" or "false" depending on whether there is information about this allele in the database. For more details see our <a href="hgBeacon" target="_blank">Beacon Server</a>.</p> <p>