dfbcbc98dac158890c1d7e9cce6338cd6d446fa5 jnavarr5 Thu Nov 21 13:10:10 2019 -0800 Creating lists of the URLs and variant types to make it easier to read, refs #24408 diff --git src/hg/makeDb/trackDb/human/lovdComp.html src/hg/makeDb/trackDb/human/lovdComp.html index 59ade22..1c5e8f6 100644 --- src/hg/makeDb/trackDb/human/lovdComp.html +++ src/hg/makeDb/trackDb/human/lovdComp.html @@ -39,84 +39,115 @@ </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: -<a href="http://www.ucl.ac.uk/ldlr/Current/" target="_blank">http://www.ucl.ac.uk/ldlr/Current/</a>, -<a href="http://brca.iarc.fr/LOVD/" target="_blank">http://brca.iarc.fr/LOVD/</a>, +<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> + <li> <a href="http://bioinf4.fcm.unicamp.br/LOVD/" - target="_blank">http://bioinf4.fcm.unicamp.br/LOVD/</a>, -<a href="http://vitigene.igib.res.in" target="_blank">http://vitigene.igib.res.in</a>, + 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>, -<a href="http://www.medgen.mcgill.ca/nndi/" target="_blank">http://www.medgen.mcgill.ca/nndi/</a>, -<a href="http://sysbio.org.cn/" target="_blank">http://sysbio.org.cn/</a>, -<a href="http://genome.igib.res.in/PGx/" target="_blank">http://genome.igib.res.in/PGx/</a>, + 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>, -<a href="http://genome.igib.res.in/tblovd/" target="_blank">http://genome.igib.res.in/tblovd/</a>, + 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/" - target="_blank">https://ab-openlab.csir.res.in/mitolsdb/</a>, -<a href="http://genome.igib.res.in/snolovd/" target="_blank">http://genome.igib.res.in/snolovd/</a>, -<a href="http://www.genomed.org/lovd2/" target="_blank">http://www.genomed.org/lovd2/</a>, -<a href="http://skingenetics.igib.res.in/" target="_blank">http://skingenetics.igib.res.in/</a>, -<a href="http://mitodyn.org/" target="_blank">http://mitodyn.org/</a>. 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> + 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> To find all LOVD databases that contain variants of a given gene, you can get a list of databases by constructing a url in the format geneSymbol.lovd.nl, for example, <a href="https://grenada.lumc.nl/LSDB_list/lsdbs/TP53" target="_blank">tp53.lovd.nl</a>. You can then use the LOVD API to retrieve more detailed information from a particular database. See the <a href="http://www.lovd.nl/3.0/faq#FAQ15">LOVD FAQ</a>.</p> <h2>Display Conventions and Configuration</h2> <p> Genomic locations of LOVD variation entries are labeled with the gene symbol and the description of the mutation according to <a href="http://www.hgvs.org/mutnomen/" target="_blank">Human Gene Variation Society standards</a>. For instance, the label AGRN:c.172G>A means that the cDNA of AGRN is mutated from G to A at position 172. </p> <p> -Since October 2017, the functional effect for variants is shown on the -details page, if annotated. The possible -values are: notClassified, functionAffected, notThisDisease, notAnyDisease, -functionProbablyAffected, functionProbablyNotAffected, functionNotAffected -unknown. LOVD does not use the term "pathogenic", please see the <a +Since October 2017, the functional effect for variants is shown on the details page, if annotated. +The possible values are: +<ul> + <li>notClassified</li> + <li>functionAffected</li> + <li>notThisDisease</li> + <li>notAnyDisease</li> + <li>functionProbablyAffected</li> + <li>functionProbablyNotAffected</li> + <li>functionNotAffected</li> + <li>unknown</li> +</ul> +LOVD does not use the term "pathogenic", please see the <a href="http://varnomen.hgvs.org/bg-material/basics/" target="_blank">HGVS Terminology page</a> for more details.</p> <p> All other information is shown on the respective LOVD variation page, accessible via the "Link to LOVD" above. </p> <h2>Methods</h2> <p> The mappings displayed in this track were provided by LOVD. </p> <h2>Credits</h2>