58f12b639fa769899cb22380678ead6325ed0499 steve Thu Aug 22 12:41:00 2013 -0700 Added announcement for new LOVD, HGMD, and UniProt Variants tracks diff --git src/hg/htdocs/indexNews.html src/hg/htdocs/indexNews.html index c490f79..f45fa18 100755 --- src/hg/htdocs/indexNews.html +++ src/hg/htdocs/indexNews.html @@ -1,43 +1,76 @@ -<!--News Section-----------------------------------------------> +<!-- News Section ============================================- --> <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%" BORDER=0> <TR><TD> <!--cheap trick to get background on row to be continuous--> <TABLE CELLPADDING=0 CELLSPACING=0 WIDTH="100%"> <TR><TD ALIGN="left"> <font size="4"><a name="TOC"></a><b> News</b></font><a href="http://www.twitter.com/GenomeBrowser" target="_blank"><img src="http://twitter-badges.s3.amazonaws.com/t_small-a.png" alt="Follow GenomeBrowser on Twitter" style="vertical-align:text-bottom; margin-left: 15px;"></a></TD> <TD ALIGN="right"><A HREF="goldenPath/newsarch.html"><IMG SRC="images/news.jpg" ALT="" ALIGN="right" BORDER=0></A> </TD></TR></TABLE> </TD></TR></TABLE> <TABLE BGCOLOR="#fffee8" WIDTH="100%" CELLPADDING=0> <TR><TH HEIGHT=3></TH></TR> <TR><TD WIDTH=10></TD> <TD> <P> To receive announcements of new genome assembly releases, new software features, updates and training seminars by email, subscribe to the <A HREF="http://groups.google.com/a/soe.ucsc.edu/group/genome-announce?hl=en" TARGET=_blank>genome-announce</A> mailing list.</P> <!-- start news --> <p> + <font face="courier" size="3"><b>22 August 2013 + - Three New Human Variation Tracks Released</b></font> + </p> + <p> + We are pleased to announce the release of three tracks that describe + human genetic variation. They are based on the + <a href="http://lovd.nl/2.0/index_list.php" target="_blank">Leiden Open + Variation Database (LOVD)</a>, the + <a href="http://www.hgmd.cf.ac.uk/ac/index.php" target="_blank">Human Gene + Mutation Database Public (HGMD)</a>, and amino acid mutations in the + <a href="http://www.uniprot.org/" target="_blank">UniProt database</a>. The + majority of the data were collected from publications by curators in the three + databases. + </p> + <p> + The three databases have varying license restrictions. UniProt provides complete + information about the mutation amino acid change, the disease and a link to the + publications that mention it. LOVD provides the mutation and a link to a website + with disease and publication details. HGMD provides some coordinates and a link to + its own website which requires registration. + </p> + <p> + These tracks are intended for use primarily by physicians and other professionals + concerned with genetic disorders, by genetics researchers, and by advanced students + in science and medicine. While the Genome Browser database is open to the public, users + seeking information about a personal medical or genetic condition are urged to consult + with a qualified physician for diagnosis and for answers to personal questions. + </p> + <p> + We'd like to thank all three databases for their help in putting the data together. The + tracks were produced at UCSC by Maximilian Haeussler and Steve Heitner. + </p> + <p> <font face="courier" size="3"><b>22 July 2013 - Variant Annotation Integrator</b></font> </p> <p> In order to assist researchers in annotating and prioritizing thousands of variant calls from sequencing projects, we have developed the Variant Annotation Integrator (VAI). Given a set of variants uploaded as a custom track (in either <a href="FAQ/FAQformat.html#format10">pgSnp</a> or <a href="goldenPath/help/vcf.html">VCF</a> format), the VAI will return the predicted functional effect (e.g., synonymous, missense, frameshift, intronic) for each variant. The VAI can optionally add several other types of relevant information, including: the <a href="https://www.ncbi.nlm.nih.gov/SNP/" target="_blank">dbSNP</a> identifier if the variant is found in dbSNP, protein damage scores for missense variants from the <a href="https://sites.google.com/site/jpopgen/dbNSFP" @@ -51,110 +84,76 @@ output formats, and annotation options, and a way to add information from any track in the Genome Browser, including custom tracks. </p> <p> There are two ways to navigate to the VAI: (1) From the "Tools" menu, follow the "Variant Annotation Integrator" link. (2) After uploading a custom track, hit the "go to variant annotation integrator" button. The user's guide is at the bottom of the page, under "Using the Variant Annotation Integrator." </p> <p> Thank you to Angie Hinrichs, Bob Kuhn, Brian Raney, Brooke Rhead, and Jonathan Casper for their input and work on this feature. </p> - <p> - <font face="courier" size="3"><b>2 July 2013 - - Assembly Data Hubs</b></font> - </p> - <p> - We are pleased to announce a new feature in the UCSC Genome Browser: - Assembly Data Hubs. - </p> - <p> - Assembly Data Hubs extend the functionality of Track Data Hubs to - assemblies that are not hosted natively on the Browser. Assembly Data - Hubs were developed to address the increasing need for researchers to - annotate sequence for which UCSC does not provide an annotation - database. They allow researchers to include the underlying reference - sequence, as well as data tracks that annotate that sequence. Sequence - is stored in the UCSC twoBit format, and the annotation tracks are - stored in the same manner as Track Data Hubs. - </p> - <p> - To read more about using Assembly Data Hubs, or about creating your - own, please see these guides: - </p> - <p> - <a href="http://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html"> - http://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html</a> - </p> - <p> - <a href="http://genomewiki.ucsc.edu/index.php/Assembly_Hubs"> - http://genomewiki.ucsc.edu/index.php/Assembly_Hubs</a> - </p> - <p> - Many thanks to Hiram Clawson, Brian Raney, and Pauline Fujita for their work on this feature. - </p> - - <!-- start archives --> <hr> <p> <!-- staged for archive use <p> + <font face="courier" size="3"><b>22 August 2013 + - Three New Human Variation Tracks Released:</b></font> We are + pleased to announce the release of three tracks that describe human + genetic variation. + <a href="goldenPath/newsarch.html#082213">Read more</a>. + </p> + + <p> <font face="courier" size="3"><b>22 July 2013 - Variant Annotation Integrator:</b></font> In order to assist researchers in annotating and prioritizing thousands of variant calls from sequencing projects, we have developed the Variant Annotation Integrator (VAI). <a href="goldenPath/newsarch.html#072213">Read more</a>. </p> + --> <p> <font face="courier" size="3"><b>2 July 2013 - Assembly Data Hubs:</b></font> Assembly Data Hubs extend the functionality of Track Data Hubs to assemblies that are not hosted natively on the Browser. <a href="goldenPath/newsarch.html#070213">Read more</a>. </p> - --> <p> <font face="courier" size="3"><b>2 July 2013 - New Gene Alleles feature on the details pages of UCSC genes:</b></font> For each protein-coding gene in the UCSC Genes track, variant data from the 2,184 (per autosome) phased chromosomes from Phase 1 of the 1000 Genomes Project have been distilled into "gene haplotype alleles." <a href="goldenPath/newsarch.html#070213b">Read more</a>. </p> <p> <font face="courier" size="3"><b>28 June 2013 - New UCSC Genes Track Released for GRCh37/hg19:</b></font> We're happy to announce the release of an updated UCSC Genes track for the GRCh37/hg19 human Genome Browser. <a href="goldenPath/newsarch.html#062813">Read more</a>. </p> <p> <font face="courier" size="3"><b>27 June 2013 - New Official European Mirror Released: </b></font> Announcing an official mirror for European users, with automatic redirection. <a href="goldenPath/newsarch.html#062713">Read more</a>. </p> - <p> - <font face="courier" size="3"><b>26 June 2013 - - Suggestion Box Released:</b></font> - Due to popular demand, we have created a suggestion box for track, assembly, - tool, and other feature requests. - <a href="goldenPath/newsarch.html#062613">Read more</a>.</p> - </TD><TD WIDTH=15> </TD></TR></TABLE> <BR></TD></TR></TABLE> </TD></TR></TABLE>