9ff1cfb85060858263a0978407de64c2715a4722
chmalee
  Fri Oct 22 11:50:35 2021 -0700
Staging orphanet track ready for QA, refs #14319

diff --git src/hg/makeDb/trackDb/human/trackDb.ra src/hg/makeDb/trackDb/human/trackDb.ra
index 2a3a571..e68fcd7 100644
--- src/hg/makeDb/trackDb/human/trackDb.ra
+++ src/hg/makeDb/trackDb/human/trackDb.ra
@@ -5422,18 +5422,33 @@
 
 track covidMuts
 type bigBed 12 + 
 shortLabel Rare Harmful Vars
 longLabel Rare variants underlying COVID-19 severity and susceptibility from the COVID Human Genetics Effort
 mouseOver $gene $name $rsId Genotype: $genotype; Zygosity: $zygo ; Inheritance: $inhMode
 labelFields gene, name
 defaultLabelFields gene, name
 noScoreFilter on
 group covid 
 color 179,0,0
 visibility hide
 bigDataUrl /gbdb/$D/covidMuts/covidMuts.bb
 multiRegionsBedUrl /gbdb/hg19/covidMuts/covidMuts.regions.bed
  
+track orphadata
+bigDataUrl /gbdb/$D/bbi/orphanet/orphadata.bb
+shortLabel Orphanet
+longLabel Orphadata: Aggregated Data From Orphanet
+group phenDis
+type bigBed 9 +
+urls ensemblID="https://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=$$" pmid="https://pubmed.ncbi.nlm.nih.gov/$$" orphaCode="http://www.orpha.net/consor/cgi-bin/OC_Exp.php?lng=en&Expert=$$" omim="https://www.omim.org/entry/$$?search=$$&highlight=$$" hgnc="https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:$$"
+skipEmptyFields on
+skipFields name,score,itemRgb
+mouseOver Gene: $geneSymbol, Disorder: $disorder, Inheritance(s): $inheritance, Onset: $onsetList
+filterValues.assnType Biomarker tested in,Candidate gene tested in,Disease-causing germline mutation(s) (gain of function) in,Disease-causing germline mutation(s) (loss of function) in,Disease-causing germline mutation(s) in,Disease-causing somatic mutation(s) in,Major susceptibility factor in,Modifying germline mutation in,Part of a fusion gene in,Role in the phenotype of
+filterValues.inheritance Autosomal dominant,Autosomal recessive,Mitochondrial inheritance,Multigenic/multifactorial,No data available,Not applicable,Oligogenic,Semi-dominant,Unknown,X-linked dominant,X-linked recessive,Y-linked
+filterValues.onsetList Adolescent,Adult,All ages,Antenatal,Childhood,Elderly,Infancy,Neonatal,No data available
+itemRgb on
+release alpha