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 @@ -1,136 +1,167 @@ <h2>Description</h2> <div class="warn-note" style="border: 2px solid #9e5900; padding: 5px 20px; background-color: #ffe9cc;"> <p><span style="font-weight: bold; color: #c70000;">NOTE:</span><br> LOVD is intended for use primarily by physicians and other professionals concerned with genetic disorders, by genetics researchers, and by advanced students in science and medicine. While the LOVD database is open to the public, users seeking information about a personal medical or genetic condition are urged to consult with a qualified physician for diagnosis and for answers to personal questions. Further, please be sure to visit the <a href = "http://www.lovd.nl/3.0/home" target="_blank">LOVD web site</a> for the very latest, as they are continually updating data.</p> <p><span style="font-weight: bold; color: #c70000;">DOWNLOADS:</span><br> LOVD databases are owned by their respective curators and are not available for download or mirroring by any third party without their permission. Batch queries on this track are only available via the UCSC Beacon API (see below). See also the <a href= "http://lovd.nl/2.0/index_list.php" target="_blank">LOVD web site</A> for a list of database installations and the respective curators. </p></div> <p> This track shows the genomic positions of all <b>public</b> entries in public installations of the Leiden Open Variation Database system (<a href="http://www.lovd.nl/3.0/home" target="_blank">LOVD</a>) and the effect of the variant, if annotated. Due to the copyright restrictions of the LOVD databases, UCSC is not allowed to host any further information. To get details on a variant (bibliographic reference, phenotype, disease, patient, etc.), follow the "Link to LOVD" to the central server at Leiden, which will then redirect you to the details page on the particular LOVD server reporting this variant. </p> <p> 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: -<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> <p> Thanks to the LOVD team, Ivo Fokkema, Peter Taschner, Johan den Dunnen, and all LOVD curators who gave permission to show their data.</p> <h2>References</h2> <p> Fokkema IF, Taschner PE, Schaafsma GC, Celli J, Laros JF, den Dunnen JT. <a href="https://onlinelibrary.wiley.com/doi/abs/10.1002/humu.21438" target="_blank"> LOVD v.2.0: the next generation in gene variant databases</a>. <em>Hum Mutat</em>. 2011 May;32(5):557-63. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/21520333" target="_blank">21520333</a> </p>