7f892f8fa5f41b18d489cfdbb0255c05b1b3e3f3 jnavarr5 Mon Oct 7 10:55:15 2019 -0700 Updating http to https for hg19, uiLinks cronjob. diff --git src/hg/makeDb/trackDb/human/lovd.html src/hg/makeDb/trackDb/human/lovd.html index dcc2796..d20719f 100644 --- src/hg/makeDb/trackDb/human/lovd.html +++ src/hg/makeDb/trackDb/human/lovd.html @@ -54,31 +54,31 @@ http://genome.igib.res.in/tblovd/, https://ab-openlab.csir.res.in/mitolsdb/, http://genome.igib.res.in/snolovd/, http://www.genomed.org/lovd2/, http://skingenetics.igib.res.in/, http://mitodyn.org/. 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">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">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="http://grenada.lumc.nl/LSDB_list/lsdbs/TP53">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>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">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,