579039309916a4c6c76ff97933b69eac88bba9ff jnavarr5 Wed May 1 14:34:54 2024 -0700 Adding more citations to the cite.html page (GenArk, REST API, GBiB, DI, VAI, LiftOver). Moving sections around because of the new additions. refs #19925 diff --git src/hg/htdocs/cite.html src/hg/htdocs/cite.html index 696d29a..c6a0913 100755 --- src/hg/htdocs/cite.html +++ src/hg/htdocs/cite.html @@ -1,128 +1,203 @@ <!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> 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. </p> <p> 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 stable resources in genomics that you can rely on. </p> <p> At the moment, the most recent UCSC Genome Browser paper has the <a target=_blank href="https://pubmed.ncbi.nlm.nih.gov/36420891/">PMID 36420891</a>, DOI 10.1093/nar/gkac1072</a>. 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 keep these identifiers short, currently they are "hg19" and "hg38" for the most common human assemblies. 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 your genomics results into the browser with <a href="https://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html">Track Hubs</a>. </p> <a name="ref"></a> <h2>Genome Browser software and website references</h2> + +<p> +<strong>Genome Browser screenshots:</strong><br> +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 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>Most recent UCSC Genome Browser publication:</strong> +<strong>Most recent UCSC Genome Browser publication:</strong><br> Nassar et al. <a href="https://pubmed.ncbi.nlm.nih.gov/36420891/" target="_blank"> The UCSC Genome Browser database: 2023 update</a>. <em>Nucleic Acids Research</em> 2023 PMID: 36420891, DOI: 10.1093/nar/gkac1072 </p> <p> -All present and past UCSC Genome Browser updates sorted by date can be shown with this -<a - target=_blank 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">PubMed search</a>. -</p> -<p> -<strong>Original UCSC Genome Browser publication:</strong> +<strong>Original UCSC Genome Browser publication:</strong><br> 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 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> +All present and past UCSC Genome Browser updates sorted by date can be shown with this +<a + target=_blank 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">PubMed search</a>. +</p> + +<hr> + <p> -<strong>BLAT:</strong> +<strong>BLAT:</strong><br> 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> +<hr> + <p> -<strong>UCSC Table Browser:</strong> +<strong>LiftOver:</strong><br> +Hinrichs AS, Karolchik D, Baertsch R, Barber GP, Bejerano G, Clawson H, Diekhans M, Furey TS, Harte +RA, Hsu F <em>et al</em>. +<a href="https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkj144" target="_blank"> +The UCSC Genome Browser Database: update 2006</a>. +<em>Nucleic Acids Res</em>. 2006 Jan 1;34(Database issue):D590-8. +</p> + +<hr> + +<p> +<strong>UCSC Table Browser:</strong><br> 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> + +<hr> + +<p> +<strong>UCSC Data Integrator and Variant Annotation Integrator:</strong><br> +Hinrichs AS, Raney BJ, Speir ML, Rhead B, Casper J, Karolchik D, Kuhn RM, Rosenbloom KR, Zweig AS, +Haussler D <em>et al</em>. +<a href="https://academic.oup.com/bioinformatics/article-lookup/doi/10.1093/bioinformatics/btv766" +target="_blank"> +UCSC Data Integrator and Variant Annotation Integrator</a>. +<em>Bioinformatics</em>. 2016 May 1;32(9):1430-2. +</p> + +<hr> + <p> -<strong>BigWig and BigBed tools:</strong> +<strong>BigWig and BigBed tools:</strong><br> 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> + +<hr> + <p> -<strong>Track Data Hubs:</strong> +<strong>RESTful API:</strong><br> +Lee CM, Barber GP, Casper J, Clawson H, Diekhans M, Gonzalez JN, Hinrichs AS, Lee BT, Nassar LR, +Powell CC <em>et al</em>. +<a href="https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkz1012" target="_blank"> +UCSC Genome Browser enters 20th year</a>. +<em>Nucleic Acids Res</em>. 2020 Jan 8;48(D1):D756-D761. +</p> + +<hr> + +<p> +<strong>Track Data Hubs:</strong><br> 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> + +<hr> + +<p> +<strong>Genome Browser in a Box (GBiB):</strong><br> +Haeussler M, Raney BJ, Hinrichs AS, Clawson H, Zweig AS, Karolchik D, Casper J, Speir ML, Haussler +D, Kent WJ. +<a href="https://academic.oup.com/bioinformatics/article-lookup/doi/10.1093/bioinformatics/btu712" +target="_blank"> +Navigating protected genomics data with UCSC Genome Browser in a Box</a>. +<em>Bioinformatics</em>. 2015 Mar 1;31(5):764-6.</p> + +<hr> + <p> -<strong>UCSC Gene Sorter:</strong> +<strong>UCSC Gene Sorter:</strong><br> 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> + +<hr> + <p> -<strong>UCSC SARS-CoV-2 Genome Browser</strong> +<strong>UCSC SARS-CoV-2 Genome Browser:</strong><br> 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> +<hr> + +<p> +<strong>GenArk: UCSC Genome Archive:</strong><br> +Clawson H, Lee BT, Raney BJ, Barber GP, Casper J, Diekhans M, Fischer C, Gonzalez JN, Hinrichs AS, +Lee CM <em>et al</em>. +<a href="https://doi.org/10.21203/rs.3.rs-2697398/v1" target="_blank"> +GenArk: Towards a million UCSC Genome Browsers</a>. +<em>Res Sq</em>. 2023 Apr 3;. +</p> + -<p><strong>Other genome assemblies:</strong> +<p><strong>Other genome assemblies:</strong><br> Manuscripts that include the use of Genome Browser assembly data from organisms other than human 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" -->