2742d9a7607a7e9f1862358779044a128b576fd4 max Thu Aug 17 02:15:18 2023 -0700 trying to improve cite.html a little, no redmine yet diff --git src/hg/htdocs/cite.html src/hg/htdocs/cite.html index fc114e4..b7a7327 100755 --- src/hg/htdocs/cite.html +++ src/hg/htdocs/cite.html @@ -1,63 +1,82 @@ <!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 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>. Permission is granted for reuse of all graphics produced -by the UCSC Genome Browser website.</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 -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> +You are free to use all graphics produced by this website in your published work or on other websites, there +is no need to contact us to request permission, see the <a href="/license/">license page</a> for details. +But the UCSC Genome Browser is exclusively funded by NIH and if research articles do +not cite or mention us, we cannot report the citations and it is harder for NIH to justify funding one of the +few long-term and stable resources in genomics. +</p> + <p> -We ask that authors cite our latest database update <a href="goldenPath/pubs.html">publications</a> -alongside any specific tools used as described below. -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> +So you can do us a great favor if you cite the most recent NAR paper, the one +at the top of this <a +href="https://pubmed.ncbi.nlm.nih.gov/?term=%28%28UCSC+Genome+Browser%5BTitle%5D%29+AND+%28update%5BTitle%5D+OR+updates%5BTitle%5D%29+AND+%22Nucleic+acids+research%22%5BJournal%5D%29+NOT+ENCODE%5BTitle%5D&sort=date&size=100>"PubMed +search.</a>. At the moment, the most recent paper has the PMID 36420891 and +the DOI 10.1093/nar/gkac1072. In addition, you can include a reference to the Genome +Browser website in your manuscript: <a href="index.html" +target="_blank">http://genome.ucsc.edu</a> or mention in the text that you used the "UCSC Genome Browser". +To cite just one of our computational tools, see the <a href="#ref">reference section</a> below. +</p> + +<p>While doing this, you can check if the genome coordinates in your paper are +clear to the readers and if you specified the genome assembly that you used. +One cannot mention the genome assembly too often. Computational +biologists will appreciate if your supplemental files with genome annotations +include the genome assembly identifier directly in the file name. We try to +keep the identifiers short, currently they are "hg19" and "hg38". In a similar +vein, references to nucleotides ideally have the full chromosome position in +your publication text somewhere or in a supplemental table, and not only the +position on the transcript and or coding sequence, as transcript models can +change a lot. +</p> + +<p>To make this even easier, when refering to a gene or genomic location, you can +use the menu <a href="../cgi-bin/hgSession">"My Data > My Sessions"</a>, to +generate a short, stable link to your current genome browser view for your +publication. In this way, readers can jump from your publication to this +genome location and get their view configured for your particular message. +You can even add your own annotations to the UCSC Genome Browser, either as +very simple text labels, by pasting a line like "chr1 1 1000 my_annotation" +into the box found under <a href="../cgi-bin/hgCustom">"My Data > Custom +Tracks"</a> or by loading all genomics results into the browser via Track Hubs. +</p> <a name="ref"></a> <p> -<h2>Genome Browser software and website</h2> +<h2>General Genome Browser software and website references</h2> <p> -<strong>UCSC Genome Browser:</strong> +<strong>Original UCSC Genome Browser publication:</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 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. We recommend including a <a -href="goldenPath/help/hgSessionHelp.html#Introduction">Session URL</a> +the most recent Genome Browser paper in the manuscript. As mentioned above, we recommend including a <a +href="goldenPath/help/hgSessionHelp.html#Introduction">My Data > My Sesssion URL</a> of your screenshot to allow readers to interact with your data and get more information.</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> @@ -75,61 +94,23 @@ 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>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> +should, e.g. one of the thousands of GenArk assemblies that we provide, should cite the relevant sequencing paper. +Usually this information can be found on the +assembly description that appears when the genome is selected on our gateway page or on the NCBI GenBank BioProject +page of the assembly.</p> <!--#include virtual="$ROOT/inc/gbPageEnd.html" -->