5d72bddf0393f961e00b2b354457fdcc8e62bc8d
lrnassar
  Thu May 22 16:36:33 2025 -0700
Updating the panelApp otto job to simplify the overall script from 3 seprate ones to a single call, and also adding support for the similar (but not identical) panelApp australia resource, refs #35758

diff --git src/hg/makeDb/trackDb/human/panelApp.alpha.ra src/hg/makeDb/trackDb/human/panelApp.alpha.ra
index df9d8f1c5d2..3ad4d516bfc 100644
--- src/hg/makeDb/trackDb/human/panelApp.alpha.ra
+++ src/hg/makeDb/trackDb/human/panelApp.alpha.ra
@@ -23,48 +23,49 @@
     skipFields chrom,chromStart,blockStarts,blockSizes,entityName,tags,status,mouseOverField
     filterValues.confidenceLevel 3,2,1,0
     priority 1
 
     track panelAppCNVs
     parent panelApp on
     shortLabel PanelApp GE CNVs
     longLabel Genomics England PanelApp CNV Regions
     type bigBed 9 +
     visibility pack
     bigDataUrl /gbdb/$D/panelApp/cnv.bb
     itemRgb on
     urls omimGene="https://www.omim.org/entry/$$" panelID="https://panelapp.genomicsengland.co.uk/panels/$$/" entityName="https://panelapp.genomicsengland.co.uk/panels/entities/$$"
     labelFields entityName
     skipEmptyFields on
+    mouseOverField mouseOverField
     skipFields chrom,chromStart,blockStarts,blockSizes
     filterValues.confidenceLevel 3,2,1,0
     priority 2
 
     track panelAppTandRep
     parent panelApp on
     shortLabel PanelApp GE STRs
     longLabel Genomics England PanelApp Short Tandem Repeats
     type bigBed 9 +
     visibility pack
     bigDataUrl /gbdb/$D/panelApp/tandRep.bb
     itemRgb on
     urls omimGene="https://www.omim.org/entry/$$" ensemblID="https://ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=$$" hgncID="https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:$$" panelID="https://panelapp.genomicsengland.co.uk/panels/$$/" geneSymbol="https://panelapp.genomicsengland.co.uk/panels/entities/$$"
-    mouseOverField mouseOverField
     labelFields hgncSymbol
     skipEmptyFields on
     skipFields chrom,chromStart,blockStarts,blockSizes,mouseOverField
     filterValues.confidenceLevel 3,2,1,0
+    mouseOver <b>Gene name:</b> $geneName<br><b>Panel:</b> $name<br><b>MOI:</b> $modeOfInheritance<br><b>Phenotypes: </b><br> $phenotypes<br><b>Confidence level:</b> $confidenceLevel
     priority 3
 
     track panelAppAusGenes
     parent panelApp on
     shortLabel PanelApp Australia Genes
     longLabel PanelApp Australia Genes Panels
     type bigBed 9 +
     visibility pack
     bigDataUrl /gbdb/$D/panelApp/genesAus.bb
     url https://panelapp-aus.org//panels/$<panelID>/gene/$<geneSymbol>/
     urlLabel Link to PanelApp Australia
     urls omimGene="https://www.omim.org/entry/$$" ensemblGenes="https://ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=$$" hgncID="https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:$$" panelID="https://panelapp-aus.org/panels/$$/" geneSymbol="https://panelapp-aus.org/panels/entities/$$"
     mouseOverField mouseOverField
     labelFields geneSymbol
     skipEmptyFields on
@@ -72,33 +73,34 @@
     filterValues.confidenceLevel 3,2,1,0
     priority 4
 
     track panelAppAusCNVs
     parent panelApp on
     shortLabel PanelApp Australia CNVs
     longLabel PanelApp Australia CNV Regions
     type bigBed 9 +
     visibility pack
     bigDataUrl /gbdb/$D/panelApp/cnvAus.bb
     itemRgb on
     urls omimGene="https://www.omim.org/entry/$$" panelID="https://panelapp-aus.org/panels/$$/" entityName="https://panelapp-aus.org/panels/entities/$$"
     labelFields entityName
     skipEmptyFields on
     skipFields chrom,chromStart,blockStarts,blockSizes
+    mouseOverField mouseOverField
     filterValues.confidenceLevel 3,2,1,0
     priority 5
 
     track panelAppAusTandRep
     parent panelApp on
     shortLabel PanelApp Australia STRs
     longLabel PanelApp Australia Short Tandem Repeats
     type bigBed 9 +
     visibility pack
     bigDataUrl /gbdb/$D/panelApp/tandRepAus.bb
     itemRgb on
     urls omimGene="https://www.omim.org/entry/$$" ensemblID="https://ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=$$" hgncID="https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:$$" panelID="https://panelapp-aus.org/panels/$$/" geneSymbol="https://panelapp-aus.org/panels/entities/$$"
-    mouseOverField mouseOverField
+    mouseOver <b>Gene name:</b> $geneName<br><b>Panel:</b> $name<br><b>MOI:</b> $modeOfInheritance<br><b>Phenotypes: </b><br> $phenotypes<br><b>Confidence level:</b> $confidenceLevel
     labelFields hgncSymbol
     skipEmptyFields on
     skipFields chrom,chromStart,blockStarts,blockSizes,mouseOverField
     filterValues.confidenceLevel 3,2,1,0
     priority 6