dd4821f6b5e8b5dd02947ee9ebf8eb0b3bedaebb
gperez2
  Mon Dec 12 16:24:58 2022 -0800
Fixing the biotype link for Non-coding transcript categorization section, refs #29789 #29790 #29791

diff --git src/hg/makeDb/trackDb/wgEncodeGencodeDisplayLift1.shared.html src/hg/makeDb/trackDb/wgEncodeGencodeDisplayLift1.shared.html
index 88e893a..b48c9b7 100644
--- src/hg/makeDb/trackDb/wgEncodeGencodeDisplayLift1.shared.html
+++ src/hg/makeDb/trackDb/wgEncodeGencodeDisplayLift1.shared.html
@@ -37,31 +37,31 @@
 
   <li> Transcript Annotation Method: filter by the method used to create the annotation
    <ul>
      <li> All - don't filter by transcript class</li>
      <li> manual - display manually created annotations, including those that are 
        also created automatically</li>
      <li> automatic - display automatically created annotations, including those that are 
        also created manually</li>
      <li> manual_only - display manually created annotations that were
        not annotated by the automatic method</li>
      <li> automatic_only - display automatically created annotations that were
        not annotated by the manual method</li>
    </ul>
    </li>
   <li> Transcript Biotype: filter transcripts by
-       <a href="https://www.gencodegenes.org/gencode_biotypes.html" target="_blank">biotype</a></li>
+       <a href="https://www.gencodegenes.org/pages/biotypes.html" target="_blank">biotype</a></li>
   <li> Support Level: filter transcripts by <a href="#tsl">transcription support level</a></li>
 </ul>
 
 <p><b>Coloring</b> for the gene annotations is based on the annotation type: </p>
 <ul>
   <li><font color="#0c0c78"><b>coding</b></font> 
   <li><font color="#006400"><b>non-coding</b></font> 
   <li><font color="#ff33ff"><b>pseudogene</b></font> 
   <li><font color="#fe0000"><b>problem</b></font>
 </ul>
 
 <h2>Methods</h2>
 
 <p>
 The GENCODE project aims to annotate all evidence-based gene features on the 
@@ -98,31 +98,31 @@
       <li> All full-length non-coding transcripts (except problem transcripts)
            with a well characterized biotype (see below) were included in the
            basic set.</li>
       <li> If there were no transcripts meeting the above criteria, then the largest non-coding
            transcript was included in the basic set (excluding problem transcripts).</li>
     </ul>
   </li>
   <li> If no transcripts were included by either the above criteria, the longest
     problem transcript is included.
   </li>
 </ul>
 
 <P>
 <b>Non-coding transcript categorization:</b> 
 Non-coding transcripts are categorized using
-their <a href="https://www.gencodegenes.org/gencode_biotypes.html" target="_blank">biotype</a>
+their <a href="https://www.gencodegenes.org/pages/biotypes.html" target="_blank">biotype</a>
 and the following criteria:
 </p>
 <ul>
   <li> well characterized: <em>antisense, Mt_rRNA, Mt_tRNA, miRNA, rRNA, snRNA, snoRNA</em></li>
   <li> poorly characterized: <em>3prime_overlapping_ncrna, lincRNA, misc_RNA, non_coding, processed_transcript, sense_intronic, sense_overlapping</em></li>
 </ul>
 
 <p>
 <b><a name="tsl">Transcription Support Level (TSL):</a></b>
 It is important that users understand how to assess transcript annotations
 that they see in GENCODE. While some transcript models have a high level of
 support through the full length of their exon structure, there are also
 transcripts that are poorly supported and that should be considered
 speculative. The Transcription Support Level (TSL) is a method to highlight the
 well-supported and poorly-supported transcript models for users. The method