1dc1b60197136ef89d70326cb8cef0664d028a25 lrnassar Thu Oct 23 15:13:49 2025 -0700 Tweaking filters based on feedback from panelApp Aus, refs #36219 diff --git src/hg/makeDb/trackDb/human/panelApp.ra src/hg/makeDb/trackDb/human/panelApp.ra index 982c9e11f9e..efadaeb83f2 100644 --- src/hg/makeDb/trackDb/human/panelApp.ra +++ src/hg/makeDb/trackDb/human/panelApp.ra @@ -1,125 +1,128 @@ track panelApp shortLabel PanelApp longLabel Genomics England and Australia PanelApp Diagnostics type bigBed 9 + visibility hide group phenDis compositeTrack on noParentConfig on showCfg on pennantIcon Updated red ../goldenPath/newsarch.html#080825 "PanelApp Australia released Aug. 08, 2025" 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/$$" panelID="https://panelapp.genomicsengland.co.uk/panels/$$/" 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 + filterValues.confidenceLevel 3|Green (3),2|Amber (2),1|Red (1),0|Red (0) + filterValuesDefault.confidenceLevel 3,2,1 filter.panelVersion 0 filterLabel.panelVersion Minimum panel version to display filterValues.panelName Mendeliome,Incidentalome,Intellectual disability syndromic and non-syndromic,Fetal anomalies,Genomic newborn screening: BabyScreen+ filterValuesDefault.panelName Mendeliome,Incidentalome filterLabel.panelName Panel Name (only 5 common shown, use all to display all panels) + filterText.name * + filterLabel.name item name: gene (panel name) filterValues.modeOfInheritance BIALLELIC,, autosomal or pseudoautosomal|BIALLELIC (autosomal/pseudoautosomal),MONOALLELIC,, autosomal or pseudoautosomal,, imprinted status unknown|MONOALLELIC (autosomal/pseudoautosomal) imprinted status unknown,MONOALLELIC,, autosomal or pseudoautosomal,, maternally imprinted (paternal allele expressed)|MONOALLELIC (autosomal/pseudoautosomal) maternally imprinted (paternal allele expressed),MONOALLELIC,, autosomal or pseudoautosomal,, paternally imprinted (maternal allele expressed)|MONOALLELIC (autosomal/pseudoautosomal) paternally imprinted (maternal allele expressed),MONOALLELIC,, autosomal or pseudoautosomal,, NOT imprinted|MONOALLELIC (autosomal/pseudoautosomal) NOT imprinted,BOTH monoallelic and biallelic,, autosomal or pseudoautosomal|BOTH monoallelic/biallelic (autosomal/pseudoautosomal),BOTH monoallelic and biallelic (but BIALLELIC mutations cause a more SEVERE disease form),, autosomal or pseudoautosomal|BOTH monoallelic/biallelic (but BIALLELIC mutations more SEVERE)(autosomal/pseudoautosomal),X-LINKED: hemizygous mutation in males,, biallelic mutations in females|X-LINKED: hemizygous mutation in males,, biallelic mutations in females,X-LINKED: hemizygous mutation in males,, monoallelic mutations in females may cause disease (may be less severe,, later onset than males)|X-LINKED: hemizygous mutation in males,, monoallelic mutations in females may cause disease,MITOCHONDRIAL|MITOCHONDRIAL,Other|Other,Unknown|Unknown 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=$$" hgncID="https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/$$" 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