456d3d32c9a2a7da9f880bb893ec56f3f9136bf8 mspeir Wed Dec 16 08:49:52 2015 -0800 Adding announcement for hgIntegrator related tables feature, refs #15544 diff --git src/hg/htdocs/indexNews.html src/hg/htdocs/indexNews.html index 619c394..116ab44 100755 --- src/hg/htdocs/indexNews.html +++ src/hg/htdocs/indexNews.html @@ -33,30 +33,59 @@ TARGET=_blank>genome-announce</A> mailing list. Please see our <a href="http://genome.ucsc.edu/blog" target=_blank>blog</a> for posts about Genome Browser tools, features, projects and more. </p> <!-- start news --> <hr> <p> <font color="#006666" size="4"><b> Happy Holidays from the UCSC Genome Browser! —</b></font> Here's a <A HREF="../cgi-bin/hgTracks?db=hg38&hgct_customText=http://hgwdev.cse.ucsc.edu/~brianlee/customTracks/testBigGenePred/testFun/customTrackLines">card</A> for you! <hr> <p> + <font color="#006666" size="4"><b>16 December 2015 — + Output from Related Tables Now Available in the Data Integrator</b></font> + <p> + In the UCSC Genome Browser database, detailed information on the annotations for many tracks + is stored in extra tables. This information can include things such identifiers + in other databases, transcript status, or other descriptive information. You can now obtain + data from these related tables in your output from the + <a href="cgi-bin/hgIntegrator">Data Integrator</a>. + </p> + + <p> + To add related tables to your Data Integrator output, first, select and add at least one + track to your data sources. Then, scroll down to the "Output Options" section and click the + <button type="button">Choose fields</button> button. + Lastly, at the bottom the section for each selected track, you will see a drop-down menu + labeled "Related tables" which allows you to select and add various tables to your output. + <p><img style="border: 1px solid black; display: block;" + src="images/hgIntegratorRelatedTablesAnnouncement.png"> + <p> + For more information about using the Data Integrator, please see the + <a href="goldenPath/help/hgIntegratorHelp.html">User Guide</a>. + </p> + + <p> + Thank you to Angie Hinrichs and Matthew Speir for their work on this feature. + </p> + + <hr> + <p> <font color="#006666" size="4"><b>9 December 2015 — Data from 1000 Genomes Project Phase 3 Now Available</b></font> <p> We have made data from Phase 3 of the <a href="http://www.1000genomes.org/" target="_blank">1000 Genomes Project</a> available for the hg19 version of the human assembly. The data includes almost 90 million variants in the form of single nucleotide variants (SNVs), insertions/deletions (InDels), and structural variants (SVs). Each variant includes a detail page that incorporates links to the variant in the dbSNP database, quality scores, and allele frequency information for various populations. More information is available on the <a href="../cgi-bin/hgTrackUi?db=hg19&g=tgpPhase3">track description page</a>. </p> <p> In addition to variant calls, the data includes two tracks that highlight regions of the @@ -94,36 +123,44 @@ Some of the available tools (not available for all assemblies or all zoom levels) are primer design and restriction enzyme predictions (Primer3Plus, Primer-BLAST, NEBCutter), mRNA and protein predictions (RegRNA 2, Riboswitches, RNAfold, PFAM), cis-regulatory predictions (Promoter 2, RSAT Metazoa), and CRISPR/Cas9 predictions (CRISPOR, CHOPCHOP), as well as links to view the region at NCBI or Ensembl. You can suggest other tools via our <a href="/cgi-bin/hgUserSuggestion">Suggestion Box</a>.</p> <p> Credit goes to Max Haeussler for implementing this new feature. </p> <hr> <!-- start archives --> <!--staged for future release <p> + <font color="#006666" size="4"><b>16 December 2015 — + Output from Related Tables Now Available in the Data Integrator</b>: </font> + You can now obtain data from these related tables in your output from the + <a href="cgi-bin/hgIntegaror">Data Integrator</a>. + <a href="goldenPath/newsarch.html#121615">Read more</a>. + </p> + + <p> <font color="#006666" size="4"><b>9 December 2015 — Data from 1000 Genomes Project Phase 3 Now Available</b>: </font> We have made data from Phase 3 of the <a href="http://www.1000genomes.org/" target="_blank">1000 Genomes Project</a> available for the hg19 version of the human assembly. - <a href="goldenPath/newsarch.html#120815">Read more</a>. + <a href="goldenPath/newsarch.html#120915">Read more</a>. </p> <p> <font color="#006666" size="4"><b>25 November 2015 — New "View - In External Tools" Menu Sends Data to Prediction Websites!</b></font> Do you often get the current sequence with "View - DNA" just to copy and paste it into another website? With the new menu "View - In External Tools" you can now send the current region to remote tools with two clicks. <a href="goldenPath/newsarch.html#112515">Read more</a>. </p> --> <p> <font color="#006666" size="4"><b>3 November 2015 — New quick links for the Genome Browser's top menu bar </b>:</font> The "Genomes" menu now features direct links to jump to browsing the human