cad83b1193fe5487f19123b9ef2ffa9c0b96a3be donnak Wed Jan 15 15:06:29 2014 -0800 Redid the format of this page to shorten it and hopefully make it more usable. Added refs for big*, track hubs, and gene sorter, and updated a few of the other entries. diff --git src/hg/htdocs/cite.html src/hg/htdocs/cite.html index c39a369..a4e56bd 100755 --- src/hg/htdocs/cite.html +++ src/hg/htdocs/cite.html @@ -1,175 +1,174 @@ <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2//EN"> <HTML> <HEAD> <META HTTP-EQUIV="Content-Type" CONTENT="text/html;CHARSET=iso-8859-1"> <TITLE>UCSC Genome Browser: Citing Us</TITLE> <LINK REL="STYLESHEET" HREF="style/HGStyle.css"> </HEAD> <BODY BGCOLOR="FFF9D2" LINK="0000CC" VLINK="#330066" ALINK="#330066"> <A NAME="TOP"></A> <TABLE BORDER=0 CELLPADDING=0 CELLSPACING=0 WIDTH="100%"> <TR><TH COLSPAN=2 ALIGN="left"><IMG SRC="images/title.jpg"></TH></TR> <TR><TD COLSPAN=2 HEIGHT=40><!--#include virtual="inc/topbar.html"--></TD></TR> <!--Content Tables-------------------------------------------------------> <TR><TD COLSPAN=2 CELLPADDING=10> <!--outer table is for border purposes--> <TABLE WIDTH="100%" BGCOLOR="#888888" BORDER="0" CELLSPACING="0" CELLPADDING="1"> <TR><TD> <TABLE BGCOLOR="fffee8" WIDTH="100%" BORDER="0" CELLSPACING="0" CELLPADDING="0"> <TR><TD> <TABLE BGCOLOR="D9E4F8" BACKGROUND="images/hr.gif" WIDTH=100%> <TR><TD> <FONT SIZE="4"><b> Citing the UCSC Browser in a Publication or Web Page</b></FONT> </TD></TR> </TABLE> <TABLE BGCOLOR="fffee8" WIDTH="100%" CELLPADDING=0> <TR><TH HEIGHT=10></TH></TR> <TR><TD WIDTH=10> </TD><TD> <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> <P> <HR> - <B>UCSC Genome Browser:</B> + <FONT SIZE="4"><B>Genome Browser Software and Website</B></FONT> <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> - <HR> - <B>UCSC Genome Browser database/data:</B> - - <P> - Karolchik D, Barber GP, Casper J, Clawson H, Cline MS, Diekhans M, Dreszer TR, - Fujita PA, Guruvadoo L, Haeussler M, Harte RA, Heitner S, Hinrichs AS, - Learned K, Lee BT, Li CH, Raney BJ, Rhead B, Rosenbloom KR, Sloan CA, Speir ML, - Zweig AS, Haussler D, Kuhn RM, Kent WJ. - <a href="http://nar.oxfordjournals.org/content/early/2013/11/21/nar.gkt1168.long" - target="_blank">The UCSC Genome Browser database: 2014 update</a>. - <em>Nucleic Acids Res</em>. 2013 Nov 21. [Epub ahead of print] - PMID: <a href="http://www.ncbi.nlm.nih.gov/pubmed/24270787" - target="_blank">24270787</a> - </p> - - <P> - 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. - </P> - - <P> - <HR> - <B>UCSC ENCODE Browser/database:</B> - - <P> - 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/content/early/2012/11/26/nar.gks1172.full" - TARGET=_blank>ENCODE Data in the UCSC Genome Browser: year 5 update</A>. - <em>Nucleic Acids Res.</em> 2012; doi: 10.1093/nar/gks1172. - </P> - - <P> - <HR> - <B>BLAT alignment tool:</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>. <em>Genome Res.</em> 2002 Apr;12(4):656-64. </P> - <P> - <HR> <B>UCSC Table Browser:</B> - <P> 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>. + <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. + <A HREF="http://bioinformatics.oxfordjournals.org/content/early/2013/11/30/bioinformatics.btt637.long" + TARGET="_blank">Track Data Hubs enable visualization of user-defined genome-wide + annotations on the UCSC Genome Browser</A>. + <em>Bioinformatics</em>. 2013 Nov 30. [Epub ahead of print] + </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>. + <em>Genome Res</em>. 2005 May;15(5):737-41. + </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> <HR> - <B>Human genome assembly:</B> + <FONT SIZE="4"><B>Genome Browser Data</B></FONT> + </P> <P> - Work pertaining to the human genome assembly should cite - the Human Genome Consortium paper: + <B>Annotation data:</B> + Karolchik D, Barber GP, Casper J, Clawson H, Cline MS, Diekhans M, Dreszer TR, + Fujita PA, Guruvadoo L, Haeussler M, Harte RA, Heitner S, Hinrichs AS, + Learned K, Lee BT, Li CH, Raney BJ, Rhead B, Rosenbloom KR, Sloan CA, Speir ML, + Zweig AS, Haussler D, Kuhn RM, Kent WJ. + <A href="http://nar.oxfordjournals.org/content/42/D1/D764.long" + target="_blank">The UCSC Genome Browser database: 2014 update</A>. + <em>Nucleic Acids Res</em>. 2014 Jan 1;42(1):D764-70. + <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>Nucleic Acids Res</em>. 2013 Jan;41(Database issue):D56-63. + </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>. - <em>Nature</em>. 2001 Feb 15;409(6822):860-921. + TARGET=_blank>Initial sequencing and analysis of the human genome</A>. + <em>Nature</em>. 2001 Feb 15;409(6822):860-921.<BR> </P> <P> - When publishing results pertaining to human genome - assemblies prior to the 22 Dec., 2001 assembly, also cite - the GigAssembler: + <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>. - <em>Genome Res</em>. 2001 Sep;11(9)1541-1548. + 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> - <HR> <B>Other genome assemblies:</B> - <P>Manuscripts that include - the use of Genome Browser assembly data from organisms - other than <em>H. sapiens</em> should cite the relevant - initial sequencing paper. Most of these references can be - found on our - <A HREF="goldenPath/pubs.html">Publications</A> web page. - </P> - <P> - <HR> - <B>Screen shots:</B> - <P> - Journal-quality screen shots of the - Genome Browser can be produced by using the PDF/PS - utility accessed via the top menu bar link 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. + 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> </TD><TD WIDTH=15></TD></TR> </TABLE> <BR></TD></TR> </TABLE> </TD></TR> </TABLE> </TD></TR> </TABLE> </BODY> </HTML>