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:murphyte@ncbi. nlm. nih. gov" 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>