407df4dbb813a74de4ca4fb2a90ba2b104b82334 Merge parents 637f4eb02e5 2ec1c55ec6f jnavarr5 Fri Feb 28 15:15:26 2025 -0800 Fixing merge conflict diff --cc src/hg/htdocs/goldenPath/newsarch.html index 3104435e109,580640303e2..1c42405e7fc --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@@ -51,80 -51,116 +51,156 @@@ </div> <p>You can sign-up to get these announcements via our <a target=_blank href="https://groups.google.com/a/soe.ucsc.edu/g/genome-announce?hl=en">Genome-announce</a> email list. We send around one short announcement email every two weeks.</p> <p>Smaller software changes are not announced here. A summary of the three-weekly release changes can be found <a target=_blank href="https://genecats.gi.ucsc.edu/builds/versions.html">here</a>. For the full list of our daily code changes head to our <a href="https://github.com/ucscGenomeBrowser/kent/commits/master" target=_blank>GitHub page</a>. Lastly, see our <a href="credits.html" target="_blank"> credits page</a> for acknowledgments of the data we host.</p> <!-- ============= 2025 archived news ============= --> <a name="2025"></a> +<a name="030125"></a> +<h2>Mar. 01, 2025 New highlight features for track hubs now available</h2> +<p> +We are happy to announce the release of new vertical highlight features for track hubs. These +settings follow exactly the same syntax and functionality as the <code>filter</code> trackDb +settings, except instead of items being excluded from the display, they are striped with a colored +background to appear "highlighted" compared to the other items in the display. +The full list of highlight trackDb settings is available on the +<a href="/goldenPath/help/trackDb/trackDbHub.html#highlight">trackDb definitions</a> page. +</p> +<p> +Please note that at this time only one higlight color is available per track, and if multiple +highlight settings are present on the same track, only items that pass ALL highlight settings will +highlighted.</p> +<p> +<b>Examples:</b> +<pre> +highlight.score 300 +</pre> +<p> +In the example above, the <code>highlight.score</code> setting allows you to highlight items based +on the value of the <code>score</code> field. Passing a value of 300 to the setting will highlight +all items with a score of 300 or above.</p> +<pre> +highlightText.name NM* +</pre> +<p> +The example above uses the <code>highlightText</code> setting which will apply a highlight on the +field <code>name</code>. Using this setting, any items that begin with <i>NM</i> are +highlighted.</p> +<pre> +highlightColor #ff0000 +</pre> +<p> +In this final example, the <code>highlightColor</code> to set the default highlight color. With +this setting, all highlight stripes will use the color red, <code>#ff0000</code>.</p> +<div class="text-center"> + <img src="../images/newsArchImages/highlightAnnouncement.png" + alt="Items in the NCBI RefSeq Historical track that begin with NM are highlighted red."> +</div> + <a name="022425"></a> + <h2>Feb. 24, 2025 enGenome VarChat track for human (hg38 and hg19)</h2> + <p> + We are happy to announce the release of the enGenome VarChat track for the + <a target="_blank" href="/cgi-bin/hgTrackUi?db=hg38&g=varChat&position=default" >hg38/GRCh38</a> + and <a target="_blank" + href="/cgi-bin/hgTrackUi?db=hg19&g=varChat&position=default">hg19/GRCh37</a> human assemblies, + available in the Variants in Papers superTrack. + <a target="_blank" href="https://varchat.engenome.com/">VarChat</a> is an open platform that + leverages the power of generative artificial intelligence to support the genomic variant + interpretation process by searching the available scientific literature for each variant and + condensing it into a brief yet informative text. + </p> + + <p> + The track shows how many papers the variant was observed in, its gene, its HGVS nomenclature, and + dbSNP rsID. Variants are color-coded based on the level of literature support, as shown in the + table below:</p> + <table> + <thead> + <tr> + <th style="border-bottom: 2px solid #6678B1;">Color</th> + <th style="border-bottom: 2px solid #6678B1;">Level of literature support</th> + </tr> + </thead> + <tbody> + <tr> + <td style="background-color: #012840; width: 50px;"></td> + <td align="left">High: at least 25 papers mention the variant</td> + </tr> + <tr> + <td style="background-color: #03738C; width: 50px;"></td> + <td align="left">Medium: between 10 and 24 papers mention the variant</td> + </tr> + <tr> + <td style="background-color: #96D2D9; width: 50px;"></td> + <td align="left">Low: fewer than 10 papers mention the variant</td> + </tr> + </tbody> + </table> + <p> + We would like to thank VarChat for providing the data to UCSC. We would also like to thank Lou + Nassar, Max Haeussler, and Gerardo Perez for their efforts on this release.</p> + + <a name="022125"></a> + <h2>Feb. 21, 2025 New AlphaMissense scores track for hg38 and hg19</h2> + <p> + We are pleased to announce the addition of AlphaMissense tracks to the hg38 and + hg19 reference genomes. AlphaMissense scores predict the pathogenicity of + missense variants for all possible single amino acid substitutions in the human + proteome. + </p> + + <p> + To access these tracks on the Genome Browser, please visit their description + pages below and change the tracks' visibility: + </p> + <ul> + <li><a target="_blank" + href="/cgi-bin/hgTrackUi?db=hg38&g=alphaMissense&position=default">AlphaMissense + on hg38/GRCh38</a></li> + <li><a target="_blank" + href="/cgi-bin/hgTrackUi?db=hg19&g=alphaMissense&position=default">AlphaMissense + on hg19/GRCh37</a></li> + </ul> + <p> + To learn more about the AlphaMissense dataset, please see the + publication by <a + href="https://www.science.org/doi/full/10.1126/science.adg7492" + target="_blank">Cheng et al. Science. 2023.</a> + </p> + + <p> + We would like to thank Google DeepMind for making the data available. We would also like to thank + Jeltje van Baren and Matthew Speir for their efforts on this release.</p> + <a name="021425"></a> <h2>Feb. 14, 2025 CIViC track for hg19 and hg38 is now available</h2> <p> We are excited to announce the release of the CIViC track for <a target="_blank" href="/cgi-bin/hgTrackUi?db=hg19&g=civic&position=default">hg19/GRCh37</a> and <a href="/cgi-bin/hgTrackUi?db=hg38&g=civic&position=default" target="_blank">hg38/GRCh38</a>. The <a target="_blank" href="https://civicdb.org/welcome"> Clinical Interpretation of Variants in Cancer</a> (CIViC) is an online database of clinically -relevant variant interpretations from expert- and crowd-sourced peer-reviewed literature, clinical +relevant variant interpretations from expert and crowd-sourced peer-reviewed literature, clinical trials, and some conference abstracts. The details page for a feature will list diseases and therapies that have been associated with a genomic variant. Visiting the CIViC page for a variant will allow browsing the Molecular Profiles associated with that variant, and in turn each Molecular Profile shows the Clinical Evidence and Assertions for various diseases and therapies. </p> <p> This track reflects the monthly data summaries published by CIViC. The latest information is always available directly on the <a href="https://civicdb.org/welcome" target="_blank">CIViC website</a> or by its <a href="https://civicdb.org/api/graphiql" target="_blank">API</a>. </p> <p> We would like to thank the CIViC contributers and organizers for curating the database and for