58f12b639fa769899cb22380678ead6325ed0499
steve
  Thu Aug 22 12:41:00 2013 -0700
Added announcement for new LOVD, HGMD, and UniProt Variants tracks
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                  <font size="4"><a name="TOC"></a><b>&nbsp; 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>
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           <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 &quot;Tools&quot;
         menu, follow the &quot;Variant Annotation Integrator&quot; link. (2)
         After uploading a custom track, hit the &quot;go to variant annotation
         integrator&quot; button. The user's guide is at the bottom of the page,
         under &quot;Using the Variant Annotation Integrator.&quot;
         </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 -->
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         <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 &quot;gene haplotype
         alleles.&quot;
         <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>
-
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