cfabc62e560b5917402da1e6d6414ba588a5367d
chmalee
  Fri Jul 31 12:37:00 2020 -0700
Add omim phenotypes to clinGen dosage tracks, refs #24818

diff --git src/hg/makeDb/trackDb/human/trackDb.clinGen.ra src/hg/makeDb/trackDb/human/trackDb.clinGen.ra
index edc0aa8..398f2f6 100644
--- src/hg/makeDb/trackDb/human/trackDb.clinGen.ra
+++ src/hg/makeDb/trackDb/human/trackDb.clinGen.ra
@@ -1,54 +1,54 @@
 track clinGenComp
 shortLabel ClinGen CNV and Dosage
 longLabel Clinical Genome Resource (ClinGen) Dosage Sensitivity Map and Structural Variants
 visibility pack
 type bigBed 9 +
 group phenDis
 itemRgb on
 compositeTrack on
 html clinGenDosage
 
     track clinGenHaplo
     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="$$" haploPMID1="https://pubmed.ncbi.nlm.nih.gov/$$/?from_single_result=$$&expanded_search_query=$$" haploPMID2="https://pubmed.ncbi.nlm.nih.gov/$$/?from_single_result=$$&expanded_search_query=$$" haploPMID3="https://pubmed.ncbi.nlm.nih.gov/$$/?from_single_result=$$&expanded_search_query=$$"
+    urls url="$$" haploPMID1="https://pubmed.ncbi.nlm.nih.gov/$$/?from_single_result=$$&expanded_search_query=$$" haploPMID2="https://pubmed.ncbi.nlm.nih.gov/$$/?from_single_result=$$&expanded_search_query=$$" haploPMID3="https://pubmed.ncbi.nlm.nih.gov/$$/?from_single_result=$$&expanded_search_query=$$" omimID="https://omim.org/entry/$$"
 
     track clinGenTriplo
     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="$$" triploPMID1="https://pubmed.ncbi.nlm.nih.gov/$$/?from_single_result=$$&expanded_search_query=$$" triploPMID2="https://pubmed.ncbi.nlm.nih.gov/$$/?from_single_result=$$&expanded_search_query=$$" triploPMID3="https://pubmed.ncbi.nlm.nih.gov/$$/?from_single_result=$$&expanded_search_query=$$"
+    urls url="$$" triploPMID1="https://pubmed.ncbi.nlm.nih.gov/$$/?from_single_result=$$&expanded_search_query=$$" triploPMID2="https://pubmed.ncbi.nlm.nih.gov/$$/?from_single_result=$$&expanded_search_query=$$" triploPMID3="https://pubmed.ncbi.nlm.nih.gov/$$/?from_single_result=$$&expanded_search_query=$$" omimID="https://omim.org/entry/$$"
 
     track clinGenCnv
     parent clinGenComp on
     shortLabel ClinGen Structural Variants
     longLabel Clinical Genome Resource (ClinGen) Structural Variants
     html clinGenSv
     type bigBed 9 +
     itemRgb on
     visibility dense
     mergeSpannedItems off
     bigDataUrl /gbdb/$D/bbi/clinGen/clinGenCnv.bb
     mouseOverField _mouseOver
     filterByRange.size on
     filterLabel.size Variant Size
     filterValues.variantType copy_number_loss|loss,copy_number_gain|gain
     filterLabel.variantType Variant Type
     filterValues.clinicalInterpretation Pathogenic|pathogenic,Benign|benign
     filterLabel.clinicalInterpretation Clinical Significance
     url https://www.ncbi.nlm.nih.gov/dbvar/variants/$$
     urlLabel NCBI DbVar:
     urls pubMed="https://pubmed.ncbi.nlm.nih.gov/$$/?from_single_result=$$&expanded_search_query=$$" clinGenId="$$"