1b1fe488b3bcf3f500a719d757b2b0a98e911f64
lrnassar
  Tue Oct 8 14:42:36 2024 -0700
Releasing ClinGen CSpec track and adding it to otto, refs #33794

diff --git src/hg/makeDb/trackDb/human/trackDb.clinGen.ra src/hg/makeDb/trackDb/human/trackDb.clinGen.ra
index 1d0bc3d..0431536 100644
--- src/hg/makeDb/trackDb/human/trackDb.clinGen.ra
+++ src/hg/makeDb/trackDb/human/trackDb.clinGen.ra
@@ -1,25 +1,26 @@
 track clinGenComp
 shortLabel ClinGen
 longLabel ClinGen curation activities (Dosage Sensitivity and Gene-Disease Validity)
 visibility hide
 type bigBed 9 +
 group phenDis
 itemRgb on
 compositeTrack on
 noParentConfig on
 html clinGen
+pennantIcon New red ../goldenPath/newsarch.html#100924 "October 9, 2024"
 
     track clinGenHaplo
     showCfg on
     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=$$&expanded_search_query=$$" PMID4="https://pubmed.ncbi.nlm.nih.gov/$$/?from_single_result=$$&expanded_search_query=$$" PMID5="https://pubmed.ncbi.nlm.nih.gov/$$/?from_single_result=$$&expanded_search_query=$$" PMID6="https://pubmed.ncbi.nlm.nih.gov/$$/?from_single_result=$$&expanded_search_query=$$" mondoID="https://monarchinitiative.org/disease/$$"
 
@@ -46,15 +47,26 @@
     visibility pack
     mouseOverField Mouseover
     urls geneSymbol="https://search.clinicalgenome.org/kb/genes/$$" ClinGenURL="https://search.clinicalgenome.org/kb/gene-validity/$$" HGNCid="https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/$$" MONDOid="https://monarchinitiative.org/disease/$$"
     skipFields 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
+
+    track clinGenCspec
+    shortLabel ClinGen VCEP Specifications
+    longLabel Clingen CSPEC Variant Interpretation VCEP Specifications
+    parent clinGenComp on
+    noScoreFilter on
+    type bigBed 9 +
+    bigDataUrl /gbdb/$D/bbi/clinGen/clinGenCspec.bb
+    visibility pack
+    mouseOver <b>Disease:</b> $disease <br><b>Panel:</b> $panel <br><b>Status:</b> $status
+    pennantIcon New red ../goldenPath/newsarch.html#100924 "October 9, 2024"