867c901f309976445e6d7db3a66cf93b194df968 Merge parents da6fa90 e930c87 kate Tue Jan 10 12:59:41 2017 -0800 Merge branch 'staticPages' of hgwdev.sdsc.edu:/data/git/kent into staticPages diff --cc src/hg/htdocs/cite.html index fbbbe7e,a757fcd..577b35c --- src/hg/htdocs/cite.html +++ src/hg/htdocs/cite.html @@@ -1,159 -1,130 +1,139 @@@ <!DOCTYPE html> <!--#set var="TITLE" value="UCSC Genome Browser: Citing Us" --> -<!--#include virtual="/gbPageStart.html"--> + +<!--#if expr="$GB_DOCUMENT_ROOT" --> +<!--#include virtual="/gbDocs/gbPageStart.html" --> +<!--#else --> +<!--#include virtual="/gbPageStart.html" --> +<!--#endif --> <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"--> +<!--#if expr="$GB_DOCUMENT_ROOT" --> +<!--#include virtual="/gbDocs/gbPageEnd.html" --> +<!--#else --> +<!--#include virtual="/gbPageEnd.html" --> +<!--#endif -->