7c6d98294ac965c787499157e31178d353caed96 jnavarr5 Fri May 23 14:48:41 2025 -0700 Commenting out the PubTator track since it isn't released yet, refs #34595 diff --git src/hg/makeDb/trackDb/human/varaico.html src/hg/makeDb/trackDb/human/varaico.html new file mode 100755 index 00000000000..33301189a64 --- /dev/null +++ src/hg/makeDb/trackDb/human/varaico.html @@ -0,0 +1,97 @@ +<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> +</div> + +<p> +<a href="https://varaico.com/" target="_blank">Varaico</a> +stands for "Variation Research Advancing Insight in Complex Organisms". Varaico 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> +<!-- 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 +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: +</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> + </tr> + <tr> + <th bgcolor="#03738C"></th> + <th align="left">Some papers mention the variant</th> + </tr> + <tr> + <th bgcolor="#96D2D9"></th> + <th align="left">Few papers mention 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> + +<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>