1afc00801fa1291d55a92e292f9fca3aa87b6566 max Mon Nov 4 05:14:23 2019 -0800 adding release tags for lovd and adding lovdComp.html, refs #24408 diff --git src/hg/makeDb/trackDb/human/lovdComp.html src/hg/makeDb/trackDb/human/lovdComp.html new file mode 100644 index 0000000..d20719f --- /dev/null +++ src/hg/makeDb/trackDb/human/lovdComp.html @@ -0,0 +1,116 @@ +<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. +UCSC does not 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> +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: +http://www.ucl.ac.uk/ldlr/Current/, +http://brca.iarc.fr/LOVD/, +http://bioinf4.fcm.unicamp.br/LOVD/, +http://vitigene.igib.res.in, +http://fishmap2.igib.res.in/mirlovd/, +http://www.medgen.mcgill.ca/nndi/, +http://sysbio.org.cn/, +http://genome.igib.res.in/PGx/, +http://www-huge.uni-regensburg.de/BEST1_database/, +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="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, +functionProbablyAffected, functionProbablyNotAffected, functionNotAffected +unknown. LOVD does not use the term "pathogenic", please see the <a +href="http://varnomen.hgvs.org/bg-material/basics/">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>