f5108b55dc2ce1a0dacfc261a89523c27440903a jnavarr5 Tue Jun 3 12:50:27 2025 -0700 Adding a track descripiton page for the varaico track to describe the colors for the track, refs #34595 diff --git src/hg/makeDb/trackDb/human/varaico.html src/hg/makeDb/trackDb/human/varaico.html index 33301189a64..46b35315616 100755 --- src/hg/makeDb/trackDb/human/varaico.html +++ src/hg/makeDb/trackDb/human/varaico.html @@ -1,97 +1,104 @@ <H2>Description</H2> <div class="warn-note" style="border: 2px solid #c70039; padding: 5px 20px; background-color: #fadbd8;"> <p><span style="font-weight: bold; color: #c70000;">NOTE:</span><br> Some rights reserved. This work permits non-commercial use, distribution and reproduction in any medium, provided the original author and source are credited. The data and code underlying this project are copyright Johannes Birgmeier. <br> -We take no responsibility for diagnoses or medical decisions based on information obtained from this -website.</p> +License and legal information can be found on the <a href="https://varaico.com/license" +target="_blank">Varaico website</a>.</p> </div> <p> <a href="https://varaico.com/" target="_blank">Varaico</a> -stands for "Variation Research Advancing Insight in Complex Organisms". Varaico was created using +(<b>Va</b>riation <b>R</b>esearch <b>A</b>dvancing <b>I</b>nsight in <b>C</b>omplex +<b>O</b>rganisms) was created using literature mining, similar to AVADA. Varaico variants are generated by an automated process that extracts purely factual information about genes from scientific papers (by matching strings against gene names) and HGVS variant descriptions (using regular expressions). Varaico aims to reduce false-positive gene and variant mentions and link them together appropriately, but nonetheless, many variants displayed are not mapped to the genomic position intended by the authors. </p> <p> For data questions, Varaico can be contacted at <A HREF="mailto:jbirgmei@gmail. com"> -jbirgmei@gmail. -com</A> +jbirgmei@gmail.com</A> <!-- above address is jbirgmei at gmail.com --> </p> <h2>Display Conventions and Configuration</h2> <p> Genomic locations of variants are labeled with the HGNC gene symbol and the variant change. Mouse over the variants to show the gene, variant, latest author/year/title, number of publications -mentioning the variant, and variant effect. Clicking on an item will provide a link directly to +mentioning the variant, and variant effect.</p> + +<p> +Clicking on an item will provide a link directly to Varaico to view all publications mentioning this variant.</p> <p> -The items are colored based on the amount of literature support as described on the table below: +The items are colored based on the amount of literature support and are a gradient from the +colors described on the table below: </p> <p> <table> <thead> <tr> <th style="border-bottom: 2px solid #6678B1;">Color</th> <th style="border-bottom: 2px solid #6678B1;">Level of literature support</th> </tr> </thead> <tr> - <th bgcolor="#3b4dc1"></th> - <th align="left">More than 20 papers mention the variant</th> + <th bgcolor="#3B4DC1"></th> + <th align="left">>20 papers mention the variant</th> + </tr> + <tr> + <th bgcolor="#B30326"></th> + <th align="left"> 20 papers mention the variant</th> + </tr> + <tr> + <th bgcolor="#F59E7F"></th> + <th align="left"> 15 papers mention the variant</th> + </tr> + <tr> + <th bgcolor="#D6DBE4"></th> + <th align="left"> 10 papers mention the variant</th> </tr> <tr> - <th bgcolor="#03738C"></th> - <th align="left">Some papers mention the variant</th> + <th bgcolor="#7EA1F9"></th> + <th align="left"> 5 papers mention the variant</th> </tr> <tr> - <th bgcolor="#96D2D9"></th> - <th align="left">Few papers mention the variant</th> + <th bgcolor="#3A4CC0"></th> + <th align="left"> 1 paper mentions the variant</th> </tr> </table> </p> <H2>Data access</H2> <p> The raw data can be explored interactively with the <a href="../cgi-bin/hgTables">Table Browser</a> or the <a href="../cgi-bin/hgIntegrator">Data Integrator</a>. The data can be accessed from scripts through our -<a href="https://api.genome.ucsc.edu">API</a>, the track name is "varChat". </p> +<a href="https://api.genome.ucsc.edu">API</a>, the track name is "varaico". </p> <p> For automated download and analysis, the genome annotation is stored in a bigBed file that can be downloaded from <a href="http://hgdownload.soe.ucsc.edu/gbdb/$db/bbi/" target="_blank">our download server</a>. The file for this track is called <tt>varaico.bb</tt>. Individual regions or the whole genome annotation can be obtained using our tool <tt>bigBedToBed</tt> which can be compiled from the source code or downloaded as a precompiled binary for your system. </p> <p> Instructions for downloading source code and binaries can be found <a href="http://hgdownload.soe.ucsc.edu/downloads.html#utilities_downloads">here</a>. The tool can also be used to obtain only features within a given range, e.g. <br><br> <tt>bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/hg38/bbi/varaico.bb -chrom=chr21 -start=0 -end=10000000 stdout</tt></p> </p> - -<H2>References</H2> -<p> -De Paoli F, Berardelli S, Limongelli I, Rizzo E, Zucca S. <a -href="https://www.ncbi.nlm.nih.gov/pubmed/38579245" target="_blank">VarChat: the generative AI -assistant for the interpretation of human genomic variations</a>. <em>Bioinformatics</em>. -2024Mar29;40(4). PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/38579245" -target="_blank">38579245</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11055464/" -target="_blank">PMC11055464</a></p>