ba9090c1767c6cab887fba49b2439f7cabc74e99
gperez2
  Tue Nov 1 17:50:58 2022 -0700
Code review edits and updates for the public hub guidelines page, refs #28424

diff --git src/hg/htdocs/goldenPath/help/publicHubGuidelines.html src/hg/htdocs/goldenPath/help/publicHubGuidelines.html
index 805eb57..88706f5 100755
--- src/hg/htdocs/goldenPath/help/publicHubGuidelines.html
+++ src/hg/htdocs/goldenPath/help/publicHubGuidelines.html
@@ -7,87 +7,87 @@
 
 <h1>Public Hub Guidelines</h1>
 <p>
 The Genome Browser provides links to a collection of public hubs that have been registered
 with UCSC and are available to view on the <a target="_blank"
 href="../../cgi-bin/hgHubConnect?#publicHubs" >Public Hubs page</a>.
 Here are guidelines for those who are trying to make a hub a UCSC public hub. If you have created a
 hub that meets the requirements and is of general interest to the research community, please
 contact us at
 <A HREF="mailto:&#103;&#101;&#110;&#111;&#109;&#101;&#45;ww&#119;&#64;&#115;&#111;&#101;.
 uc&#115;&#99;.
 &#101;&#100;&#117;">
 &#103;&#101;&#110;&#111;&#109;&#101;&#45;ww&#119;&#64;&#115;&#111;&#101;.uc&#115;&#99;.&#101;&#100;&#117;
 </A> to have it added to the list.
 
-<p>As a reference for interpreting trackDb.txt settings use the Hub Track Database Definition <a 
+<p>As a reference for interpreting trackDb.txt settings, use the Hub Track Database Definition <a
 target="_blank" href="trackDb/trackDbHub.html#loc">glossary</a>. For information on using the Track
 Hub features, refer to the <a href="hgTrackHubHelp.html">Genome Browser Track Hub User Guide</a>.
 See also the <a href="hubQuickStart.html" target="_blank">Basic Hub Quick Start Guide</a>, <a
 href="hubQuickStartGroups.html" target="_blank">Quick Start Guide to Organizing Track Hubs into 
 Groupings</a>, <a href="https://genome-blog.soe.ucsc.edu/blog/2022/06/28/track-hub-settings/"
 target="_blank">Track hub settings blog post</a>, <a href="hubQuickStartAssembly.html"
 target="_blank">Quick Start Guide to Assembly Hubs</a> and <a href="hubQuickStartSearch.html"
 target="_blank">Quick Start Guide to Searchable Track Hubs</a>.</p>
 </p>
 
 <h2>Contents</h2>
 
 <h6><a href="#requiredGuidelines">Required Guidelines</a></h6>
 <h6><a href="#recommendedGuidelines">Recommended Guidelines</a></h6>
 <h6><a href="#publicHubExamples">Public Hub Examples</a></h6>
 
 <a id="requiredGuidelines"></a>
 <h2>Required Guidelines</h2>
 <p>The following guidelines must be met before your hub will be added to our public list:</p>
 <p style="text-indent: 20px"><b>Required for both track and assembly hubs:</b></p>
 <ul>
  <li>You MUST have a description page for every configuration page (composite, superTrack or stand
      alone track). Note that multiple tracks and/or composites can use the same description page
      with the <a target="_blank" href="trackDb/trackDbHub.html#html">"html" setting</a>. You can
      find more information on creating track description pages in the
      <a href="#recommendedGuidelines">recommendations</a> section below.
  </li>
  <li>All of your description pages MUST have a contact email address prominently displayed.
  </li>
  <li>Try to have no more than 10 tracks with <a target="_blank"
-     href="trackDb/trackDbHub.html#visibility">visibility</a> set to display (in full, pack, dense,
-     or squish) as default upon first connecting your hub.
+     href="trackDb/trackDbHub.html#visibility">visibility</a> set to display (in full, pack, squish,
+     or dense) as default upon first connecting your hub.
  </li>
  <li>Have a descriptionUrl html page specified in your hub.txt. This should be a URL to a description
      page for your entire hub, often public hubs will link to a full-text paper or to their
      laboratory webpage that describes the research presented in the hub. These links are presented
      on the Public Hubs page as a hyperlink on the longLabel presented in the hub.txt, while the
      shortLabel is a hyperlink to the hub.txt location.
  </li>
 </ul>
 
 <p style="text-indent: 20px"><b>Required for only assembly hubs:</b></p>
 <ul>
  <li>Add a gateway page for each assembly by having a htmlPath line for each genome not already
      hosted by UCSC in the <a target="_blank"
      href="http://genomewiki.ucsc.edu/index.php/Assembly_Hubs#genomes.txt">genomes.txt</a>.
  </li>
  <li>The following settings should properly be set in your genomes.txt (The last 3 settings will make
      it easier to find assembly hub species in hgGateway by UI search):
  </li>
- <ol>
+ <ul>
   <li>defaultPos</li>
   <li>scientificName</li>
   <li>organism</li>
   <li>description</li>
- </ol>
+ </ul>
 </ul>
 
 <a id="recommendedGuidelines"></a>
 <h2>Recommended Guidelines</h2>
 <p>These guidelines in the following sections are recommended to improve user experience, but are
    not required to be implemented before the hub is added to our list of Public Hubs.</p>
 <h3>Track organization recommendations</h3>
 <p>
 Related tracks can be grouped in a few different ways, namely <a href="trackDb/trackDbHub.html#superTrack"
 target="_blank">superTracks</a>, <a href="trackDb/trackDbHub.html#aggregate"
 target="_blank">multiWigs</a>, and <a href="trackDb/trackDbHub.html#compositeTrack"
 target="_blank">composites</a>. If your hub includes a large number of tracks, the grouping of
 tracks may be necessary. This will prevent your hub's track group from being an overwhelming mess
 of individual tracks and can make user configuration of your tracks easier.</p>
 
@@ -101,60 +101,60 @@
      more than one view. Views ideally give alternate access to the same data (e.g. signals and
      called peaks). Keep in mind that the value of views is that they allow for more than one
      data/configuration type (e.g. bigBed and bigWig) in a single composite. All subtracks of a
      view must have the same data type. Likewise, all subtracks of a non-multi-view composite must
      be the same type.</li>
  <li>Recommendations for using dimensions with your composite tracks:</li>
   <ol>
   <li>There should be no <a href="trackDb/trackDbHub.html#dimensions" target="_blank">
       dimensions</a> with a single entry (do not have only one cell line represented in dimX=cell),
       unless data growth is expected to fill in additional entries.</li>
   <li>Using only one dimension: preferably use dimX (e.g. dimensions dimX=cell). This saves vertical
       User Interface space, but is not always the best choice.</li>
   <li>Using two dimensions: use dimX and dimY (e.g. dimensions dimX=cell dimY=mark)</li>
   <li>Using more than two: use dimX, dimY on the most important dimensions. Then use dimA,B,C as
       needed on lesser dimensions. (e.g. dimensions dimX=cell dimY=mark dimA=donor_id)</li>
-  <li>The A,B,C.. dimensions should probably use <a href="trackDb/trackDbHub.html#filterComposite"
+  <li>The A,B,C dimensions should probably use <a href="trackDb/trackDbHub.html#filterComposite"
       target="_blank">filterComposite</a> (e.g. filterComposite dimA)</li>
   <li>Each dimension and views should be represented in sortOrder, ideally in order of dimX, dimY,
       dimA,B,C, view (e.g. sortOrder cell_type=+ mark=+ donor_id=+ view=+).
   <li>Tags of subGroup/dimension should be short and sweet with no special chars. Also labels can
       have HTML codes embedded (e.g. NOT CPG_methylation_%=CPG_methylation_% RATHER
-      mpct=CPG_methylation_&_#37</li>
+      mpct=CPG_methylation_&_#37)</li>
   <li>Never represent the same subgroup in both view and as a dimension (e.g. NOT dimensions
       dimX=view). A subgroup should never be in two dimensions (e.g. NOT dimensions
       dimX=cell dimY=mark dimA=cell). The composite will appear to function but multiple ways of
-      selecting the same thing will create a confusing and inconsistent User Interface.</li>   
+      selecting the same thing will create a confusing and inconsistent user interface.</li>
  </ol>
 </ul>
 
 <h6>Super tracks</h6>
 <p>
 Extremely large hubs may use  <a href="trackDb/trackDbHub.html#superTrack"
 target="_blank">superTracks</a> as well to achieve a meaningful hierarchy. Super tracks
 can be used to group together any type of related tracks; for example, you could combine a multiWig,
-a composite and a bigBed track together into a single superTrack.</p>
+a composite, and a bigBed track together into a single superTrack.</p>
 
 <h3>Track display recommendations</h3>
 <ul>
  <li>Avoid setting a composite track and all of its subtracks to the same visibility. When you have
      composite tracks that are hidden by default, it is best to still designate some subtracks to
      display when the composite track is turned on (visibility dense, versus the default of hide).
      This provides an example of your track data to users who turn on your composite track. If no
      subtracks are turned on by default, a user who changes your composite track visibility to
      "show" won't see anything.</li>
- <li>The shortLabel text should be under 17 characters, or meaningful information may be cut off
+ <li>The shortLabel text should be under 20 characters, or meaningful information may be cut off
      from display when tracks are set to "dense" visibility.</li>
 </ul>
 
 <h3>Track description page recommendations</h3>
 <ul>
  <li>The description page should preferably contain UCSC's standard track description, Display
      Conventions and Configuration, Methods, Credits, and References. More information can be
      found on the <a href="examples/hubExamples/templatePage.html"
      target="_blank">template page</a>.</li>
  <li>Your track description pages should provide meaningful documentation for your tracks.
  <ol>
  <li>If you are creating a hub based on a paper, use the paper's abstract as a starting point for
      your track's description section</li>
  <li>The Methods section expand upon the overview of the Description section and provide more
      details about how the data for the track was produced</li>