97805fb2ceb73357aa78aa94107148dc355d4e1c mspeir Tue Sep 22 08:36:22 2026 -0700 Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> diff --git src/hg/makeDb/trackDb/phastConsElements.html src/hg/makeDb/trackDb/phastConsElements.html index 7091fb714f3..10ee5711f0e 100644 --- src/hg/makeDb/trackDb/phastConsElements.html +++ src/hg/makeDb/trackDb/phastConsElements.html @@ -26,30 +26,38 @@ subject to certain constraints on the "coverage" of the genome by conserved elements and the "smoothness" of the conservation scores. Details can be found in Siepel <em>et al</em>. (2005).</P> <P> The predicted conserved elements are segments of the alignment that are likely to have been "generated" by the conserved state of the phylo-HMM. Each element is assigned a log-odds score equal to its log probability under the conserved model minus its log probability under the non-conserved model. The "score" field associated with this track contains transformed log-odds scores, taking values between 0 and 1000. (The scores are transformed using a monotonic function of the form a * log(x) + b.) The raw log odds scores are retained in the "name" field and can be seen on the details page or in the browser when the track's display mode is set to "pack" or "full".</P> +<h2>Data Access</h2> +<p> +The conserved elements can be retrieved for a single region or for a list of regions with the <a +href="hgTables">Table Browser</a>, and joined with other annotations in the <a +href="hgIntegrator">Data Integrator</a>. For automated access, they are also served by our <a +href="../goldenPath/help/api.html">REST API</a>. +</p> + <H2>Credits</H2> <P> This track was created at UCSC using the following programs: <UL> <LI>Blastz and multiz by Minmei Hou, Scott Schwartz and Webb Miller of the <A HREF="http://www.bx.psu.edu/miller_lab/" TARGET=_blank>Penn State Bioinformatics Group</A>. <LI>AxtBest, axtChain, chainNet, netSyntenic, and netClass by Jim Kent at UCSC. <LI>PhastCons by Adam Siepel at Cornell University. </UL> </P> <H2>References</H2> <H3>PhastCons</H3> <P>