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/cat/felCat3/phastConsElements4way.html src/hg/makeDb/trackDb/cat/felCat3/phastConsElements4way.html
index 18018b9674d..3458be37d80 100644
--- src/hg/makeDb/trackDb/cat/felCat3/phastConsElements4way.html
+++ src/hg/makeDb/trackDb/cat/felCat3/phastConsElements4way.html
@@ -25,30 +25,46 @@
 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?db=felCat3&amp;hgta_group=compGeno&amp;hgta_track=phastConsElements4way">Table
+Browser</a>, and joined with other annotations in the <a href="hgIntegrator?db=felCat3">Data
+Integrator</a>. For automated access, they are also served by our <a
+href="../goldenPath/help/api.html">REST API</a>.
+</p>
+<p>
+The files behind this track can be downloaded from our download server:
+<ul>
+  <li><a href="https://hgdownload.soe.ucsc.edu/goldenPath/felCat3/phastCons4way/"
+  target="_blank">PhastCons conservation scores and conserved elements</a></li>
+</ul>
+</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.ccbb.psu.edu/" 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>