b0c17e134726b4a4111fef680ae14c563220f998 gperez2 Tue Jan 7 20:56:04 2025 -0800 Code review edits for the NCBI Gene Orthologs track description, refs #35020 diff --git src/hg/makeDb/trackDb/human/refSeqComposite.html src/hg/makeDb/trackDb/human/refSeqComposite.html index 5d940ee..7ab9527 100644 --- src/hg/makeDb/trackDb/human/refSeqComposite.html +++ src/hg/makeDb/trackDb/human/refSeqComposite.html @@ -76,32 +76,39 @@ <li> <em>RefSeq Historical</em> – previous RefSeq transcript versions, including NM_ accessions and HGVS searches. This track is only available on hg38. </li> <li> <em>NCBI Orthologs</em> – Orthologous genes were identified by <a target="_blank" href="https://www.ncbi.nlm.nih.gov/refseq/annotation_euk/process/"> NCBI's Eukaryotic Genome Annotation Pipeline</a> for the NCBI Gene dataset using a combination of protein sequence similarity and local synteny analysis. Orthology is determined between the genome being annotated and a reference genome, such as human or zebrafish, and pairs of orthologs are grouped together. Transitive relationships are inferred within each group, for example, zebrafish <-> human <-> mouse. For more information on how NCBI calculates orthologs, see the details provided <a target="_blank" href="https://www.ncbi.nlm.nih.gov/kis/info/how-are-orthologs-calculated/"> - here</a>. This track is available for the following assemblies: hg38, mm39, danRer11, canFam6, - and bosTau9. + here</a>. This track is available for the following assemblies: + <a href="/cgi-bin/hgTrackUi?db=hg38&g=refSeqComposite&position=default" target="_blank">hg38</a>, + <a href="/cgi-bin/hgTrackUi?db=mm39&g=refSeqComposite&position=default" target="_blank">mm39</a>, + <a href="/cgi-bin/hgTrackUi?db=danRer11&g=refSeqComposite&position=default" + target="_blank">danRer11</a>, + <a href="/cgi-bin/hgTrackUi?db=canFam6&g=refSeqComposite&position=default" + target="_blank">canFam6</a>, and + <a href="/cgi-bin/hgTrackUi?db=bosTau9&g=refSeqComposite&position=default" + target="_blank">bosTau9</a>. </li> </ul> </dl> <p> The <em>RefSeq All</em>, <em>RefSeq Curated</em>, <em>RefSeq Predicted</em>, <em>RefSeq HGMD</em>, <em>RefSeq Select/MANE</em> and <em>UCSC RefSeq</em> tracks follow the display conventions for <a href="../goldenPath/help/hgTracksHelp.html#GeneDisplay" target="_blank">gene prediction tracks</a>. The color shading indicates the level of review the RefSeq record has undergone: predicted (light), provisional (medium), or reviewed (dark), as defined by <a target=_blank href="https://www.ncbi.nlm.nih.gov/books/NBK21091/table/ch18.T.refseq_status_codes/?report=objectonly">RefSeq</a>. </p> <p> <table> <thead>