e69a819c8711dd9fe6f8e475e1591ea41516106f jnavarr5 Fri Aug 1 13:09:47 2025 -0700 Announcing the PubTator track for hg38 and hg19, refs #35957 diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index 7bf6187c402..7479d24c1c2 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -52,30 +52,48 @@ <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="080125"></a> +<h2>Aug. 01, 2025 PubTator Variants track for human, hg38 and hg19</h2> +<p> +We are excited to announce the release of the PubTator Variants track for human assemblies, +<a href="/cgi-bin/hgTrackUi?db=hg38&position=default&g=pubtator">hg38</a> and +<a href="/cgi-bin/hgTrackUi?db=hg19&position=default&g=pubtator">hg19</a>. These tracks were created +using PubTator3 data and is freely accessible to the research community. PubTator3 is a web-based +system that offers a comprehensive set of features and tools that allow researchers to extensively +explore the ever-expanding wealth of biomedical literature for knowledge discovery. It uses advanced +text mining and state-of-the-art AI techniques to annotate and unify bio-entities and their +corresponding relations for semantic and relation searches.</p> +<p> +We would like to thank the PubTator 3.0 authors for generating and making the data publically +available. We would also like to thank Max Haeussler and Johannes Birgmeier for creating the tracks, +and Jairo Navarro the release of the tracks. +</p> + + <a name="073125"></a> <h2>July 31, 2025 New bedMethyl and bigMethyl track type</h2> <p> We are excited to announce support for a new track format for visualizing DNA methylation data: <a href="https://www.encodeproject.org/data-standards/wgbs/" target="_blank">bedMethyl</a>. This format, and its binary-indexed counterpart, <b>bigMethyl</b>, is designed to represent methylation calls from bisulfite sequencing or similar methods at single-base resolution across the genome.</p> <p> The <a href="help/bedMethyl.html" target="_blank">bedMethyl</a> format extends the standard <a href="/FAQ/FAQformat.html#format1" target="_blank">BED 9 format</a> to include additional fields such as coverage, percent methylation, and the number of modified and canonical bases. When viewed in the Genome Browser, hovering over or clicking an item reveals these additional details. Items are color-coded from <b><font color="#0000FF">0%</font></b> methylated (blue) to