8e903dc32b2ee82114c67f6f43c89311b3f6db2d
jnavarr5
  Tue May 20 15:10:04 2025 -0700
Adding the HTML 'varsInPubs.html' to the subtracks in the supertrack that were missing. Adding the number of publications and variant effect to the Varaico mouseover. Bolding items in the mouseover, refs #34595

diff --git src/hg/makeDb/trackDb/human/trackDb.ra src/hg/makeDb/trackDb/human/trackDb.ra
index 9067cc22223..28236932f34 100644
--- src/hg/makeDb/trackDb/human/trackDb.ra
+++ src/hg/makeDb/trackDb/human/trackDb.ra
@@ -165,92 +165,97 @@
         visibility dense
         type bigBed 9 +
         urls url=$$
         bigDataUrl /gbdb/$D/bbi/mastermind.bb
         noScoreFilter on
         exonNumbers off
         mouseOverField _mouseOver
         itemRgb on
         filter.mmcnt1 0
         filter.mmcnt2 0
         filter.mmcnt3 0
         dataVersion /gbdb/$D/bbi/mastermindRelease.txt
         parent varsInPubs pack
         maxWindowCoverage 40000
         maxItems 1000000
+        html varsInPubs.html
 
         track avada
         shortLabel Avada Variants
         longLabel Avada Variants extracted from full text publications
         visibility dense
         type bigBed 9 +
         bigDataUrl /gbdb/$D/bbi/avada.bb
         noScoreFilter on
         exonNumbers off
         #itemRgb on
         dataVersion release 1
         parent varsInPubs pack
         urls pmid="https://www.ncbi.nlm.nih.gov/pubmed/$$" doi="https://doi.org/$$" ensId="http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?g=$$" entrezs="https://www.ncbi.nlm.nih.gov/gene/$$" refSeq="https://www.ncbi.nlm.nih.gov/nuccore/$$"
         mouseOverField _mouseOver
+        html varsInPubs.html
 
         track varChat
         shortLabel enGenome VarChat
         longLabel enGenome VarChat: Literature match and variant's summary
         visibility dense
         type bigBed 9 + 4
         bigDataUrl /gbdb/$D/bbi/varChat.bb
         noScoreFilter on
         exonNumbers off
         parent varsInPubs pack
         maxWindowCoverage 40000
         maxItems 1000000
         mouseOverField _mouseOver
         url https://varchat.engenome.com/search?source=ucsc&text=$<VariantUrl>
         urlLabel Open Variant on VarChat
         bedNameLabel Nucleotide Change
         skipFields Variant,VariantUrl,score
         detailsDynamicTable VariantDetails|Variant Details
         dataVersion /gbdb/$D/bbi/varChatVersion.txt
         pennantIcon New red ../goldenPath/newsarch.html#022425 "Released Feb. 24, 2025"
+        html varChat.html
 
         track pubtator
         shortLabel PubTator variants
         longLabel dbSNP variants and other genetic variants grounded to dbSNP by tmVar; collected by PubTator3
         visibility dense
         type bigBed 9 +
         bigDataUrl /gbdb/$D/pubs2/pubtatorDbSnp.bb
         noScoreFilter on
         exonNumbers off
         itemRgb on
         parent varsInPubs pack
         urls pubmedIds="https://www.ncbi.nlm.nih.gov/pubmed/$$"
         mouseOver $name found in ${numPubmedIds} PubMed articles
+        html varsInPubs.html
 
         track varaico
         release alpha
         shortLabel Varaico Variants
         longLabel Varaico Variants extracted from full text publications, titles, and abstracts
         visibility dense
         type bigBed 9 +
         bigDataUrl /gbdb/$D/bbi/varaico.bb
         noScoreFilter on
         exonNumbers off
         # itemRgb on
         dataVersion release 1
         parent varsInPubs pack
         urls outlink="$$" selectedPmid="https://www.ncbi.nlm.nih.gov/pubmed/$$" rgene="https://www.ncbi.nlm.nih.gov/nuccore/$$"
-        mouseOver $hgncSymbol $variantOrigStrs in: $author ($journal, $year) - $title
+        mouseOver <b>$hgncSymbol $variantOrigStrs</b> in: $author ($journal, $year) - $title <br> <b>Number of publications:</b> $pmidCount <br> <b>Variant Effect:</b> $variantEffect
+        html varsInPubs.html
 
 track caseControl
 compositeTrack on
 shortLabel Case Control
 longLabel Case Control Consortium
 group phenDis
 visibility hide
 type chromGraph
 minMax 0,15
 linesAt 5,10
 
     track cccTrendPvalBd
     parent caseControl
     shortLabel CCC Bipolar Dis
     longLabel Case Control Consortium Bipolar Disorder Trend -log10 P-value