cf0ef0620d7fb30bf0d9813f8afd8fbc9c6613f9 jnavarr5 Fri Feb 14 13:41:24 2025 -0800 Adding a link to the CIViC website and API documentation, refs #34371 diff --git src/hg/makeDb/trackDb/human/civic.html src/hg/makeDb/trackDb/human/civic.html index be3e07d7702..9bbd692de37 100644 --- src/hg/makeDb/trackDb/human/civic.html +++ src/hg/makeDb/trackDb/human/civic.html @@ -1,102 +1,103 @@ <h2>Description</h2> <p> 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-reviewed literature, clinical trials, and some conference abstracts. </p> <p> Each variant's interpretation is in the context of a broader 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> <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> <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 various diseases and therapies. </p> <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> <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> <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. </p> <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. +latest information is always available directly on the <a href="https://civicdb.org/welcome" +target="_blank">CIViC website</a> +or by its <a href="https://civicdb.org/api/graphiql" target="_blank">API</a>. </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>, via the track name "civic". </p> <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. </p> <h2>Credits</h2> <p> Thanks to the CIViC contributers and organizers for curating the database and making the data available for download. </p> <h2>Reference</h2> <p> Griffith M, Spies NC, Krysiak K, McMichael JF, Coffman AC, Danos AM, Ainscough BJ, Ramirez CA, Rieke DT, Kujan L <em>et al</em>. <a href="https://www.ncbi.nlm.nih.gov/pubmed/28138153" target="_blank">CIViC is a community knowledgebase for expert crowdsourcing the clinical interpretation of variants in cancer</a>. <em>Nat Genet</em>. 2017Jan31;49(2):170-174. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/28138153" target="_blank">28138153</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5367263/" target="_blank">PMC5367263</a> </p>