e5b6fab7e4e0f80843313e3b7a143265249527e8
gperez2
  Wed Aug 6 16:21:54 2025 -0700
Updating the PanelApp Genes track description and fixing the hgncID urls, refs #35758

diff --git src/hg/makeDb/trackDb/human/panelApp.alpha.ra src/hg/makeDb/trackDb/human/panelApp.alpha.ra
index b23da885bb3..2ea8c9b988d 100644
--- src/hg/makeDb/trackDb/human/panelApp.alpha.ra
+++ src/hg/makeDb/trackDb/human/panelApp.alpha.ra
@@ -1,120 +1,120 @@
 track panelApp
 shortLabel PanelApp
 longLabel Genomics England and Australia PanelApp Diagnostics
 type bigBed 9 +
 visibility hide
 group phenDis
 compositeTrack on
 noParentConfig on
 showCfg on
 
     track panelAppGenes
     parent panelApp on
     shortLabel PanelApp GE Genes
     longLabel Genomics England PanelApp Genes
     type bigBed 9 +
     visibility pack
     bigDataUrl /gbdb/$D/panelApp/genes.bb
     itemRgb on
     url https://panelapp.genomicsengland.co.uk/panels/$<panelID>/gene/$<geneSymbol>/
     urlLabel Link to PanelApp
     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:$$" panelID="https://panelapp.genomicsengland.co.uk/panels/$$/" geneSymbol="https://panelapp.genomicsengland.co.uk/panels/entities/$$"
     mouseOver <b>Gene:</b> $entityName<br><b>Panel:</b> $panelName<br><b>MOI:</b> $modeOfInheritance<br><b>Phenotypes: </b> $phenotypes<br><b>Confidence level:</b> $confidenceLevel
     labelFields geneSymbol
     skipEmptyFields on
     skipFields chrom,chromStart,blockStarts,blockSizes,entityName,tags,status,mouseOverField
     filterValues.confidenceLevel 3,2,1,0
     priority 1
     filter.panelVersion 1
     filterLabel.panelVersion Minimum panel version to display
 
     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
     mouseOver <b>Gene:</b> $entityName<br><b>Panel:</b> $panelName<br><b>MOI:</b> $modeOfInheritance<br><b>Phenotypes: </b> $phenotypes<br><b>Confidence level:</b> $confidenceLevel
     skipFields chrom,chromStart,blockStarts,blockSizes
     filterValues.confidenceLevel 3,2,1,0
     priority 2
     filter.versionCreated 1
     filterLabel.versionCreated Minimum panel version to display
 
     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/$$"
+    urls omimGene="https://www.omim.org/entry/$$" ensemblID="https://ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=$$" hgncID="https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/$$" panelID="https://panelapp.genomicsengland.co.uk/panels/$$/" geneSymbol="https://panelapp.genomicsengland.co.uk/panels/entities/$$"
     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> $phenotypes<br><b>Confidence level:</b> $confidenceLevel
     priority 3
     filter.version 1
     filterLabel.version Minimum panel version to display
 
     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/$$"
     mouseOver <b>Gene:</b> $entityName<br><b>Panel:</b> $panelName<br><b>MOI:</b> $modeOfInheritance<br><b>Phenotypes: </b> $phenotypes<br><b>Confidence level:</b> $confidenceLevel
     labelFields geneSymbol
     skipEmptyFields on
     skipFields chrom,chromStart,blockStarts,blockSizes,entityName,tags,status,mouseOverField
     filterValues.confidenceLevel 3,2,1,0
     filter.panelVersion 0
     filterLabel.panelVersion Minimum panel version to display
     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
     mouseOver <b>Gene:</b> $entityName<br><b>Panel:</b> $panelName<br><b>MOI:</b> $modeOfInheritance<br><b>Phenotypes: </b> $phenotypes<br><b>Confidence level:</b> $confidenceLevel
     filterValues.confidenceLevel 3,2,1,0
     filter.versionCreated 0
     filterLabel.versionCreated Minimum panel version to display
     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/$$"
+    urls omimGene="https://www.omim.org/entry/$$" ensemblID="https://ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=$$" hgncID="https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/$$" panelID="https://panelapp-aus.org/panels/$$/" geneSymbol="https://panelapp-aus.org/panels/entities/$$"
     mouseOver <b>Gene name:</b> $geneName<br><b>Panel:</b> $name<br><b>MOI:</b> $modeOfInheritance<br><b>Phenotypes: </b> $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
     filter.version 0
     filterLabel.version Minimum panel version to display