b04b513f9f81bf519c8e31d851fcc37fb5094c25 dschmelt Fri Jan 22 11:06:23 2021 -0800 Adding new covid citation, sprucing up doc #26737 diff --git src/hg/htdocs/cite.html src/hg/htdocs/cite.html index 30d7c62..6b88dd1 100755 --- src/hg/htdocs/cite.html +++ src/hg/htdocs/cite.html @@ -1,122 +1,133 @@ <!DOCTYPE html> <!--#set var="TITLE" value="UCSC Genome Browser: Citing Us" --> <!--#set var="ROOT" value="." --> <!-- Relative paths to support mirror sites with non-standard GB docs install --> <!--#include virtual="$ROOT/inc/gbPageStart.html" --> <h1>Citing the UCSC Browser in a Publication or Web Page</h1> <p> -Follow these citation guidelines when using applications from the Genome Browser tool suite or +Follow these citation guidelines when using the Genome Browser tool suite or data from the UCSC Genome Browser database in a research work that will be published in a journal or on the Internet. In addition to the relevant paper, please include a reference to the Genome Browser website in your manuscript: <a href="index.html" -target="_blank">http://genome.ucsc.edu/</a>. Be sure to mention the release date of the genome -assembly used in your work to facilitate the examination of your data by reviewers and readers.</p> +target="_blank">http://genome.ucsc.edu</a>.</p> <p> +Be sure to mention the release date of the genome +assembly used in your work to facilitate the examination of your data by reviewers and readers. If you would like to add a URL to the Genome Browser displaying a specific location or configuration, please use a <a -href="goldenPath/help/hgSessionHelp.html#Introduction">session URL</a>. This will ensure +href="goldenPath/help/hgSessionHelp.html#Introduction">Session URL</a>. This will ensure all data and settings remain fixed. Please do <strong>not</strong> include references to our development servers (such as genome-test.soe.ucsc.edu) in published links or URLs.</p> <p> -For an extended list of publications produced by the UCSC Genome Bioinformatics group, see our +For an extended list of publications produced by the UCSC Genome Browser group, see our <a href="goldenPath/pubs.html">Publications</a> page. It is worth noting that as of April 1, 2020, Genome Browser papers have been cited 37,500 times in the literature. We thank authors for the acknowledgement of our efforts.</p> <a name="ref"></a> <p> <h2>Genome Browser software and website</h2> <p> <strong>UCSC Genome Browser:</strong> Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM, Haussler D. <a href="http://www.genome.org/cgi/content/abstract/12/6/996" target="_blank">The human genome browser at UCSC</a>. <em>Genome Res.</em> 2002 Jun;12(6):996-1006.</p> <p> +<strong>Genome Browser screenshots:</strong> +Journal-quality screenshots of the Genome Browser can be produced by using the View ->PDF/PS +utility in the top navigation bar from the tracks page. When including a +screenshot in your manuscript, reference <em>http://genome.ucsc.edu</em> in the caption and cite +the Genome Browser paper in the manuscript. Don't forget to mention the genome assembly used to +produce the image. When including a Genome Browser URL, please remove the <em>hgsid</em> parameter. +It is an internally-used parameter that expires after about a day.</p> + +<p> <strong>BLAT:</strong> Kent WJ. <a href="http://www.genome.org/cgi/content/abstract/12/4/656" target="_blank">BLAT - the BLAST-like alignment tool</a>. <em>Genome Res.</em> 2002 Apr;12(4):656-64.</p> <p> <strong>UCSC Table Browser:</strong> Karolchik D, Hinrichs AS, Furey TS, Roskin KM, Sugnet CW, Haussler D, Kent WJ. <a href="http://nar.oupjournals.org/cgi/content/abstract/32/suppl_1/D493?ijkey=06tIQcBr2VZNz&keytype=ref" target="_blank">The UCSC Table Browser data retrieval tool</a>. <em>Nucleic Acids Res</em>. 2004 Jan 1;32(Database issue):D493-6.</p> <p> <strong>BigWig and BigBed tools:</strong> Kent WJ, Zweig AS, Barber G, Hinrichs AS, Karolchik D. <a href="http://bioinformatics.oxfordjournals.org/content/26/17/2204.long" target="_blank">BigWig and BigBed: enabling browsing of large distributed data sets</a>. <em>Bioinformatics</em>. 2010 Sep 1;26(17):2204-7.</p> <p> <strong>Track Data Hubs:</strong> Raney BJ, Dreszer TR, Barber GP, Clawson H, Fujita PA, Wang T, Nguyen N, Paten B, Zweig AS, Karolchik D, Kent WJ. <a href="http://bioinformatics.oxfordjournals.org/content/30/7/1003" target="_blank">Track Data Hubs enable visualization of user-defined genome-wide annotations on the UCSC Genome Browser</a>. <em>Bioinformatics</em>. 2014 Apr 1;30(7):1003-5. Epub 2013 Nov 13.</p> <p> <strong>UCSC Gene Sorter:</strong> Kent WJ, Hsu F, Karolchik D, Kuhn RM, Clawson H, Trumbower H, Haussler D. <a href="http://www.genome.org/cgi/content/abstract/15/5/737" target="_blank">Exploring relationships and mining data with the UCSC Gene Sorter</a>. <em>Genome Res</em>. 2005 May;15(5):737-41.</p> <p> -<strong>Genome Browser screen shots:</strong> -Journal-quality screen shots of the Genome Browser can be produced by using the PDF/PS utility -accessed via the View menu in the top navigation bar on the tracks display page. When including a -screen shot in your manuscript, reference <em>http://genome.ucsc.edu</em> in the caption and cite -the Genome Browser paper in the manuscript. Don't forget to mention the genome assembly used to -produce the image. When including a Genome Browser URL, please remove the <em>hgsid</em> parameter. -It is an internally-used parameter that expires after about a day.</p> +<strong>UCSC SARS-CoV-2 Genome Browser</strong> +Fernandes JD, Hinrichs AS, Clawson H, et al. +<a href="https://www.nature.com/articles/s41588-020-0700-8" +target="_blank">The UCSC SARS-CoV-2 Genome Browser</a>. +<em>Nat Genet.</em> 2020 Sept 9; 52:991-998.</p> + + + <h2>Genome Browser data</h2> <p> <strong>Annotation data:</strong> Cite the most recent UCSC Genome Browser update in the Nucleic Acids Research "Database" issue. A list of these papers can be found using this tailored <a href="https://www.ncbi.nlm.nih.gov/pubmed/?term=((UCSC+Genome+Browser%5BTitle%5D)+AND+ (update%5BTitle%5D+OR+updates%5BTitle%5D)+AND+%22Nucleic+acids+research%22%5BJournal%5D)+NOT+ ENCODE%5BTitle%5D" target="_blank">PubMed search</a>. Be sure to sort the page by "Most Recent". <em>(Cite this paper for annotation data extracted from the Genome Browser database. Annotation tracks should also be credited according to their source, which can be found on the track's description page or on the Genome Browser <a href="goldenPath/credits.html">Credits</a> page.</em>) </p> <p> <strong>ENCODE annotation data:</strong> Rosenbloom KR, Sloan CA, Malladi VS, Dreszer TR, Learned K, Kirkup VM, Wong MC, Maddren M, Fang R, Heitner SG, Lee BT, Barber GP, Harte RA, Diekhans M, Long JC, Wilder SP, Zweig AS, Karolchik D, Kuhn RM, Haussler D, Kent WJ. <a href="http://nar.oxfordjournals.org/cgi/pmidlookup?view=long&pmid=23193274" target="_blank">ENCODE data in the UCSC Genome Browser: year 5 update</a>. <em>Nucleic Acids Res</em>. 2013 Jan;41(Database issue):D56-63.</p> <p> <strong>Human genome assembly:</strong> The Genome Sequencing Consortium. <a href="http://www.nature.com/nature/journal/v409/n6822/abs/409860a0.html" target="_blank">Initial sequencing and analysis of the human genome</a>. <em>Nature</em>. 2001 Feb 15;409(6822):860-921.</p> <p> <strong>Very early human genome assemblies:</strong> Kent WJ, Haussler D. <a href="http://www.genome.org/cgi/content/abstract/GR-1832Rv1" target="_blank">Assembly of the working draft of the human genome with gigAssembler</a>. <em>Genome Res</em>. 2001 Sep;11(9)1541-1548.<BR> <em> Cite this paper when publishing results pertaining to human genome assemblies prior to the 22 Dec. 2001 assembly.</em></p> <p> <strong>Other genome assemblies:</strong> Manuscripts that include the use of Genome Browser assembly data from organisms other than human should cite the relevant initial sequencing paper. Often this information can be found on the Genome Browser <a href="goldenPath/credits.html">Credits</a> page or on the GenBank BioProject page for the organism.</p> <!--#include virtual="$ROOT/inc/gbPageEnd.html" -->