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 Gene name: $geneName
Panel: $name
MOI: $modeOfInheritance
Phenotypes:
$phenotypes
Confidence level: $confidenceLevel
priority 3
track panelAppAusGenes
parent panelApp on
shortLabel PanelApp Australia Genes
longLabel PanelApp Australia Genes Panels
type bigBed 9 +
visibility pack
bigDataUrl /gbdb/$D/panelApp/genesAus.bb
url https://panelapp-aus.org//panels/$/gene/$/
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 Gene name: $geneName
Panel: $name
MOI: $modeOfInheritance
Phenotypes:
$phenotypes
Confidence level: $confidenceLevel
labelFields hgncSymbol
skipEmptyFields on
skipFields chrom,chromStart,blockStarts,blockSizes,mouseOverField
filterValues.confidenceLevel 3,2,1,0
priority 6