f48d6722539eedb842d629cb7c8681ad88e1b685 donnak Wed Dec 28 23:39:25 2016 -0800 First pass at migration to new style sheet. Refs #18504 diff --git src/hg/htdocs/cite.html src/hg/htdocs/cite.html index 40f94d2..a757fcd 100755 --- src/hg/htdocs/cite.html +++ src/hg/htdocs/cite.html @@ -1,150 +1,130 @@ <!DOCTYPE html> <!--#set var="TITLE" value="UCSC Genome Browser: Citing Us" --> <!--#include virtual="/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 -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 faciliate the examination of your data by -reviewers and the readers. Please do <B>not</B> include -references to our development servers (such as -genome-test.cse.ucsc.edu) in published links or URLs.</P> -<P> -For an extended list of publications produced by the UCSC -Genome Bioinformatics group, see our -<A HREF="goldenPath/pubs.html">Publications</A> page.</P> -<A NAME="ref"></A> +Follow these citation guidelines when using applications from 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 faciliate the +examination of your data by reviewers and the readers. Please do <b>not</b> include references to +our development servers (such as genome-test.cse.ucsc.edu) in published links or URLs.</p> +<p> +For an extended list of publications produced by the UCSC Genome Bioinformatics group, see our +<a href="goldenPath/pubs.html">Publications</a> page.</p> -<P> +<a name="ref"></a> +<p> <h2>Genome Browser Software and Website</h2> -<P> -<B>UCSC Genome Browser:</B> -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> +<b>UCSC Genome Browser:</b> +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> -<B>BLAT:</B> +<p> +<b>BLAT:</b> Kent WJ. -<A HREF="http://www.genome.org/cgi/content/abstract/12/4/656" -TARGET=_blank>BLAT - the BLAST-like alignment tool</A>. +<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> -<P> -<B>UCSC Table Browser:</B> -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> -<B>BigWig and BigBed tools:</B> +<p> +<b>UCSC Table Browser:</b> +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> +<b>BigWig and BigBed tools:</b> 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>. +<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> -<B>Track Data Hubs:</B> -Raney BJ, Dreszer TR, Barber GP, Clawson H, Fujita PA, Wang T, Nguyen N, Paten -B, Zweig AS, Karolchik D, Kent WJ. +</p> +<p> +<b>Track Data Hubs:</b> +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>. +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> -<B>UCSC Gene Sorter:</B> +</p> +<p> +<b>UCSC Gene Sorter:</b> 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>. +<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> -<B>Genome Browser screen shots:</B> +</p> +<p> +<b>Genome Browser screen shots:</b> 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> -<P> +<em>hgsid</em> parameter. It is an internally-used parameter that expires after about a day. +</p> +<p> <h2>Genome Browser Data</h2> -</P> -<P> -<B>Annotation data:</B> -Rosenbloom KR, Armstrong J, Barber GP, Casper J, Clawson H, Diekhans M, -Dreszer TR, Fujita PA, Guruvadoo L, Haeussler M, Harte RA, Heitner S, -Hickey G, Hinrichs AS, Hubley R, Karolchik D, Learned K, Lee BT, Li CH, -Miga KH, Nguyen N, Paten B, Raney BJ, Smit AF, Speir ML, Zweig AS, +</p> +<p> +<b>Annotation data:</b> +Rosenbloom KR, Armstrong J, Barber GP, Casper J, Clawson H, Diekhans M, Dreszer TR, Fujita PA, +Guruvadoo L, Haeussler M, Harte RA, Heitner S, Hickey G, Hinrichs AS, Hubley R, Karolchik D, +Learned K, Lee BT, Li CH, Miga KH, Nguyen N, Paten B, Raney BJ, Smit AF, Speir ML, Zweig AS, Haussler D, Kuhn RM, Kent WJ. <a href="http://nar.oxfordjournals.org/content/43/D1/D670.long" target="_blank"> The UCSC Genome Browser database: 2015 update</a>. <em>Nucleic Acids Res</em>. 2015 Jan;43(Database issue):D670-81. -PMID: <a href="http://www.ncbi.nlm.nih.gov/pubmed/25428374" -target="_blank">25428374</a>; PMC: <a -href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4383971/" -target="_blank">PMC4383971</a> +PMID: <a href="http://www.ncbi.nlm.nih.gov/pubmed/25428374" target="_blank">25428374</a>; +PMC: <a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4383971/" target="_blank">PMC4383971</a> <BR> -<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> -<B>ENCODE annotation data:</B> -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>(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> +<b>ENCODE annotation data:</b> +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> -<B>Human genome assembly:</B> +</p> +<p> +<b>Human genome assembly:</b> 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>. +<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.<BR> -</P> -<P> -<B>Very early human genome assemblies:</B> +</p> +<p> +<b>Very early human genome assemblies:</b> 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>. +<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> -<B>Other genome assemblies:</B> -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 +<em> Cite this paper when publishing results pertaining to human genome assemblies prior to the +22 Dec. 2001 assembly.</em> +</p> +<p> +<b>Other genome assemblies:</b> +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> +</p> <!--#include virtual="/gbPageEnd.html"-->