cb4c5ca53034c40e1255903d5c993aff2c49d053 jnavarr5 Mon Feb 10 16:09:38 2025 -0800 Adding a link to the CIViC website to the track description page. Fixing a few typos in the text. Replacing double quotes with the HTML entity. refs #34371 diff --git src/hg/makeDb/trackDb/human/civic.html src/hg/makeDb/trackDb/human/civic.html index 434564da711..0bca5656f8c 100644 --- src/hg/makeDb/trackDb/human/civic.html +++ src/hg/makeDb/trackDb/human/civic.html @@ -1,87 +1,89 @@ <h2>Description</h2> <p> -This track shows genomic locations for variants in the CIViC (Clinical -Interpretation of Variants in Cancer) database. These clinically +This track shows genomic locations for variants in the +<a href="https://civicdb.org/welcome" target="_blank">CIViC (Clinical +Interpretation of Variants in Cancer) database</a>. These clinically relevant variant interpretations are expert- and crowd-sourced from peer-revied literature, clinical trials, and some conference abstracts. <p> Each variant's interpretation is in the context of a broder molecular profile: one or more variants grouped together. For example, clinical evidence may be relevant to a KRAS G12 mutation on its own, but other clinical evidence may relevant for cases with either a mutation in KRAS G12 or G13. <p> The primary points of data from the scientific literature are curated as Clinical Evidence, which connects to a molecular profile, which in turn connects to the variants shown in this track. Groups of evidence can become curator Assertions about the relevence of a molecular profile. <p> The detail for a feature will list diseases and therapies that have been associated with a genomic variant. Visiting the CIViC page for a variant will allow browsing the Molecular Profiles associated with that variant, and in turn each Molecular Profile shows the Clinical -Evidence and Assertions for variou diseases and therapies. +Evidence and Assertions for various diseases and therapies. <h2>Display Conventions and Configuration</h2> <p> There are three types of variant feature types in CIViC: gene, fusion, and factor, of which only the gene and fusion fetaures have a genomic location. <p> Gene variants are shown as a single item, with a name indicating the variant's mode: sequence change, gene expression, gene deletion, etc. <p> Fusion variants connect two genes via a structural DNA rearrangement, typically in the introns or promotors of genes. For CIViC fusions that have an annotated transcript and exon, the exon will be shown as a thick bar. If there is an intron associated with the fusion, it will be annotated as a thin bar on the feature. <h2>Data updates</h2> <p> This track reflects the monthly data summaries published by CIViC. The latest information is always available directly on the CIViC website or by its API. <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>, via the track name "civic". +accessed from scripts through our <a href="https://api.genome.ucsc.edu">API</a>, via the track name +"civic". <h2>Methods</h2> <p> The monthly CIViC Variant Summaries were reformatted at UCSC to <a href="../goldenPath/help/bigBed.html">bigBed</a> format. The data is updated every month, the week after CIViC data summary release. The diseases and therapies associated with a variant are collected from the corresponding TSV files from CIViC, using the molecular profile summaries as a mapping. <h2>Credits</h2> <p> Thanks to the CIViC contributers and organizers for curating the database and making the data available for download. <h2>Reference</h2> <p> Malachi Griffith, Nicholas C Spies, Kilannin Krysiak, Joshua F McMichael, Adam C Coffman, Arpad M Danos, Benjamin J Ainscough, Cody A Ramirez, Damian T Rieke, Lynzey Kujan, Erica K Barnell, Alex H Wagner, Zachary L Skidmore, Amber Wollam, Connor J Liu, Martin R Jones, Rachel L Bilski, Robert Lesurf, Yan-Yang Feng, Nakul M Shah, Melika Bonakdar, Lee Trani, Matthew Matlock, Avinash Ramu, Katie M Campbell, Gregory C Spies, Aaron P Graubert, Karthik Gangavarapu, James M Eldred, David E Larson, Jason R Walker, Benjamin M Good, Chunlei Wu, Andrew I Su, Rodrigo Dienstmann, Adam A Margolin, David Tamborero, Nuria Lopez-Bigas, Steven J M Jones, Ron Bose, David H Spencer, Lukas D Wartman, Richard K Wilson, Elaine R Mardis & Obi L Griffith. <a href="https://www.nature.com/articles/ng.3774">CIViC is a community knowledgebase for expert crowdsourcing the clinical interpretation of variants in cancer</a>. <em>Nature Genetics</em>. 2017 Jan 31; 49, 170-174. PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/28138153/">28138153</a>; PMCID: <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC5367263/">PMC5367263</a>