9c2c393cc048d73c20ef64cd54dde1ad559f1135
gperez2
  Wed Jun 9 10:51:14 2021 -0700
Adding a data access section to the refSeqFuncElems track, refs #27662

diff --git src/hg/makeDb/trackDb/refSeqFuncElems.html src/hg/makeDb/trackDb/refSeqFuncElems.html
index 3895e73..c4e0a40 100644
--- src/hg/makeDb/trackDb/refSeqFuncElems.html
+++ src/hg/makeDb/trackDb/refSeqFuncElems.html
@@ -1,83 +1,94 @@
 <h2>Description</h2>
 <p>
 NCBI recently announced a new release of
 <a href="https://www.ncbi.nlm.nih.gov/refseq/functionalelements/" 
 target="_blank"> functional regulatory elements</a>.
 
 NCBI is now providing 
 <a href="https://www.ncbi.nlm.nih.gov/refseq/" target="_blank" >RefSeq</a> and 
 <a href="https://www.ncbi.nlm.nih.gov/gene/" target="_blank" >Gene</a>
 records for non-genic functional elements that have been described in the literature and are 
 experimentally validated. Elements in scope include experimentally-verified gene regulatory 
 regions (e.g., enhancers, silencers, locus control regions), known structural elements
 (e.g., insulators, DNase I hypersensitive sites, matrix/scaffold-associated regions), 
 well-characterized DNA replication origins, and clinically-significant sites of DNA recombination
 and genomic instability. Priority is given to genomic regions that are implicated in human disease 
 or are otherwise of significant interest to the research community. Currently, the scope of this 
 project is restricted to human and mouse. The current scope does not include functional elements
 predicted from large-scale epigenomic mapping studies, nor elements based on disease-associated 
 variation.</p>
 
 <h2>Display Conventions and Configuration</h2>
 <p>
 Functional elements are colored by <a href="http://www.sequenceontology.org/"
                                       target=_blank>Sequence Ontology (SO)</a> term
 using the same scheme as NCBI's Genome Data Viewer:
   <ul>
     <li><span style="color: #008080"><b>Regulatory elements</b></span>
       (items labeled by <a href="http://www.insdc.org/controlled-vocabulary-regulatoryclass"
                            target=_blank>INSDC regulatory class</a>)
     <li><span style="color: #b00000"><b>Protein binding sites</b></span>
       (items labeled by bound moiety)
     <li><span style="color: #0000b0"><b>Mobile elements</b></span>
     <li><span style="color: #a0522d"><b>Recombination features</b></span>
     <li><span style="color: #b000b0"><b>Sequence features</b></span>
     <li><span style="color: #000000"><b>Other</b></span>
   </ul>
 </p>
 
 <h2>Methods</h2>
 <p>
 NCBI manually curated features in accordance with International Nucleotide 
 Sequence Database Collaboration (INSDC) standards. Features that are supported by direct 
 experimental evidence include at least one experiment qualifier with an evidence code (ECO ID) 
 from the Evidence and Conclusion Ontology, and at least one citation from PubMed. Currently
 971 distinct PubMed citations are included in this track. 
 </p>
 
 <h2>Contact</h2>
 <p>
 This track was made with assistance from
 <a href="mailto:&#109;&#117;r&#112;h&#121;&#116;&#101;&#64;&#110;&#99;&#98;&#105;.
 	&#110;lm.
 	&#110;&#105;&#104;.
 	&#103;&#111;v" target="_blank">Terence Murphy</a> at NCBI.</p>
 
+<h2>Data access</h2>
+<p>
+The raw data can be explored interactively with the <a href="/cgi-bin/hgTables"
+target="_blank">Table Browser</a>, or the <a href="/cgi-bin/hgIntegrator"
+target="_blank">Data Integrator</a>. For automated analysis, the data may be 
+queried from our <a href="../goldenPath/help/api.html" target="_blank">REST API</a>,
+and the genome annotations are stored in files that can be downloaded from our 
+<a href="https://hgdownload.soe.ucsc.edu/gbdb/hg38/ncbiRefSeq/"
+target="_blank">download server</a>, with more information available on
+<a target="_blank" href="http://genome.ucsc.edu/blog/tag/mysql/">our blog</a>.</p>
+
 <h2>New Version Available</h2>
 <p>
 Several new enhancements to the RefSeq Functional Elements dataset are available as a Public Hub.
 The hub can be found <a href="/cgi-bin/hgHubConnect?hubSearchTerms=RefSeqFE">on the Public Hub page</a>.
 The track hub was prepared by Dr. Catherine M. Farrell, NCBI/NLM/NIH with further insights discussed
 <a href="https://ncbiinsights.ncbi.nlm.nih.gov/2020/08/04/new-interaction-data-downloads-track-hub-refseq-functional-elements/"
 target="_blank">in a  related NCBI blog post</a>.</p>
 
 <h2>References</h2>
 <p>
 Pruitt KD, Brown GR, Hiatt SM, Thibaud-Nissen F, Astashyn A, Ermolaeva O, Farrell CM, Hart J,
 Landrum MJ, McGarvey KM <em>et al</em>.
 <a href="https://academic.oup.com/nar/article/42/D1/D756/1051112/RefSeq-an-update-on-mammalian-
 reference-sequences" target="_blank">RefSeq: an update on mammalian reference sequences</a>.
 <em>Nucleic Acids Res</em>. 2014 Jan;42(Database issue):D756-63.
 PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/24259432" target="_blank">24259432</a>; PMC: <a
 href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3965018/" target="_blank">PMC3965018</a>
 </p>
 
 <p>
 Pruitt KD, Tatusova T, Maglott DR.
 <a href="https://academic.oup.com/nar/article/33/suppl_1/D501/2505241/NCBI-Reference-Sequence-
 RefSeq-a-curated-non" target="_blank">NCBI Reference Sequence (RefSeq): a curated non-redundant
 sequence database of genomes, transcripts and proteins</a>.
 <em>Nucleic Acids Res.</em> 2005 Jan 1;33(Database issue):D501-4.
 PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/15608248" target="_blank">15608248</a>; PMC: <a
 href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC539979/" target="_blank">PMC539979</a>
 </p>