41c63e4b0795abf47b9fcbaf7554da7f50741ad5 lrnassar Fri Jul 19 16:29:55 2024 -0700 Sprucing up the cite.html page with general improvements and organization, refs #31996 diff --git src/hg/htdocs/cite.html src/hg/htdocs/cite.html index c6a0913..9f0359e 100755 --- src/hg/htdocs/cite.html +++ src/hg/htdocs/cite.html @@ -1,64 +1,73 @@ <!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> +<b>You are free to use all graphics produced by this website in your published work or on other websites</b>, +there is no need to contact us to request permission. See the <a href="/license/">license page</a> for details.</p> + +<h2>How to cite the UCSC Genome Browser</h2> +<p> +The UCSC Genome Browser is exclusively funded by the NIH, please consider citing us properly +so that we may report usage and continue to develop this resource.</p> +<h3>What manuscript to cite?</h3> +<p> +Please cite our latest paper, currently <a target=_blank +href="https://pubmed.ncbi.nlm.nih.gov/36420891/">PMID 36420891</a>, +DOI 10.1093/nar/gkac1072. In addition, you can reference 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 one of our +computational tools, see the <a href="#ref">reference section</a> below.</p> + +<h3>General best practices for publications</h3> +<p> +The following are recommendations to improve communication in your +scientific manuscript and ensure readers in 10 years can still find the +DNA sequence that you analyzed. This requires mention of the assembly, +chromosome position, any transcripts, and ideally also a +Genome Browser stable link:</p> +<ol> +<li><b>Assembly:</b> Provide a clear mention of which genome assembly you are working with, e.g. +"hg19" or "hg38". It is often helpful to place the assembly name directly on +any supplemental file names if they contain annotations. E.g. "promoters.hg38.bed".</li> +<li><b>Chromosome Position:</b> References to nucleotides should have full chromosome positions in the +publication text or a supplemental table, whenever possible. Including only the position on the +transcript or coding sequence can be confusing later as transcript models change. +E.g. mention "NC_000023.11:g.32389644G>A", in addition to the transcript-based +description "NM_004006.2:c.4375C>T". Or, in the manuscript, you can add the chromosome +location in brackets, such as "(hg38,chr11:32389644)", when nucleotide 4375 of +NM_004006.2 is discussed.</li> +<li><b>Transcript:</b> Transcripts change. Always mention the accession of a transcript, not only the gene name. E.g "NM_004006.2", not just +"the longest transcript of the gene DMD". Gene symbols and transcripts change over time, so any sort of accession is helpful. +<li><b>Stable links:</b> A UCSC Genome Browser link is a great way to +share results or regions of +interest in a way readers and reviewers can explore. It includes the assembly, position, all transcripts, +any tracks visible, all filter settings that you made and any other settings in the browser. +If you would like to include +a link, do not copy the URL directly from the address bar, the one with +"hgsid=xxx". These links are long and expire after a few days. +Instead, use the menu option <a href="../cgi-bin/hgSession">"My Data > My +Sessions"</a>, to generate a short, +stable link to your current genome browser view. For more information on how to add your +own annotations to share this way see <a href="../cgi-bin/hgCustom">Custom Tracks</a> +and <a href="https://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html">Track Hubs</a>.</li> +</ol> <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><br>