579d4220eec5e357b78dc0deb459db6d1858af20
chmalee
  Mon Sep 14 12:06:57 2020 -0700
Add ClinGen Gene Disease validity track to new clingen composite, refs Ana email

diff --git src/hg/makeDb/trackDb/human/trackDb.clinGen.ra src/hg/makeDb/trackDb/human/trackDb.clinGen.ra
index 9980b4c..bd662ce 100644
--- src/hg/makeDb/trackDb/human/trackDb.clinGen.ra
+++ src/hg/makeDb/trackDb/human/trackDb.clinGen.ra
@@ -1,35 +1,58 @@
 track clinGenComp
 shortLabel ClinGen
 longLabel Clinical Genome Resource (ClinGen) Dosage Sensitivity Map
 visibility pack
 type bigBed 9 +
 group phenDis
 itemRgb on
 compositeTrack on
 html clinGen
 
     track clinGenHaplo
     priority 1
     parent clinGenComp on
     shortLabel ClinGen Haploinsufficiency
     longLabel ClinGen Dosage Sensitivity Map - Haploinsufficiency
     visibility pack
     type bigBed 9 +
     bigDataUrl /gbdb/$D/bbi/clinGen/clinGenHaplo.bb
     mouseOverField _mouseOver
     filterValues.haploScore 0|No evidence available,1|Little evidence for dosage pathogenicity,2|Some evidence for dosage pathogenicity,3|Sufficient evidence for dosage pathogenicity,30|Gene associated with autosomal recessive phenotype,40|Dosage sensitivity unlikely
     filterLabel.haploScore Dosage Sensitivity Score
     urls url="$$" PMID1="https://pubmed.ncbi.nlm.nih.gov/$$/?from_single_result=$$&expanded_search_query=$$" PMID2="https://pubmed.ncbi.nlm.nih.gov/$$/?from_single_result=$$&expanded_search_query=$$" PMID3="https://pubmed.ncbi.nlm.nih.gov/$$/?from_single_result=$$&expanded_search_query=$$" omimID="https://omim.org/entry/$$"
 
     track clinGenTriplo
     priority 2
     parent clinGenComp on
     shortLabel ClinGen Triplosensitivity
     longLabel ClinGen Dosage Sensitivity Map - Triplosensitivity
     visibility pack
     type bigBed 9 +
     bigDataUrl /gbdb//$D/bbi/clinGen/clinGenTriplo.bb
     mouseOverField _mouseOver
     filterValues.triploScore 0|No evidence available,1|Little evidence for dosage pathogenicity,2|Some evidence for dosage pathogenicity,3|Sufficient evidence for dosage pathogenicity,30|Gene associated with autosomal recessive phenotype,40|Dosage sensitivity unlikely
     filterLabel.triploScore Dosage Sensitivity Score
     urls url="$$" PMID1="https://pubmed.ncbi.nlm.nih.gov/$$/?from_single_result=$$&expanded_search_query=$$" PMID2="https://pubmed.ncbi.nlm.nih.gov/$$/?from_single_result=$$&expanded_search_query=$$" PMID3="https://pubmed.ncbi.nlm.nih.gov/$$/?from_single_result=$$&expanded_search_query=$$" omimID="https://omim.org/entry/$$"
+
+    track clinGenGeneDisease
+    priority 3
+    parent clinGenComp on
+    type bigBed 9 +
+    shortLabel ClinGen Validity
+    longLabel ClinGen Gene-Disease Validity Classification
+    bigDataUrl /gbdb/$D/bbi/clinGen/clinGenGeneDisease.bb
+    visibility pack
+    mouseOverField Mouseover
+    urls ClinGenURL="https://search.clinicalgenome.org/kb/gene-validity/$$" HGNCid="https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/$$" MONDOid="https://monarchinitiative.org/disease/$$"
+    #skipFields score,strand,thickStart,thickEnd,Mouseover
+    sepFields MONDOid,SOPversion
+    itemRgb on
+    noScoreFilter on
+    searchIndex name,geneSymbol,HGNCid,MONDOid,Classification
+    filterValues.Inheritance Autosomal Dominant,Autosomal Recessive,Semidominant,X-Linked,X-linked recessive,Other
+    filterLabel.Inheritance Inheritance Pattern
+    filterValues.SOPversion SOP4,SOP5,SOP6,SOP7
+    filterLabel.SOPversion ClinGen SOP Version Number
+    filterValues.Classification Definitive,Strong,Moderate,Limited,Animal Model Only,No Reported Evidence,Disputed,Refuted
+    filterLabel.Classification ClinGen Gene-Disease Validity Classification
+    bedNameLabel Associated Disease