4654fecc7b9d5d905365bd72fee9d3fa4cb6724f
chmalee
  Thu Jan 13 12:38:46 2022 -0800
Staging updates to clingen tracks: slightly rework the otto job after changes to the clinGen website, get out links on description pages correct, refs #28453

diff --git src/hg/makeDb/trackDb/human/trackDb.clinGen.ra src/hg/makeDb/trackDb/human/trackDb.clinGen.ra
index de4e744..1d0bc3d 100644
--- src/hg/makeDb/trackDb/human/trackDb.clinGen.ra
+++ src/hg/makeDb/trackDb/human/trackDb.clinGen.ra
@@ -1,60 +1,60 @@
 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
 
     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=$$" omimID="https://omim.org/entry/$$"
+    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=$$" mondoID="https://monarchinitiative.org/disease/$$"
 
     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=$$&expanded_search_query=$$" 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=$$" omimID="https://omim.org/entry/$$"
+    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=$$" mondoID="https://monarchinitiative.org/disease/$$"
 
     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/$$"
-    #skipFields score,strand,thickStart,thickEnd,Mouseover
+    urls geneSymbol="https://search.clinicalgenome.org/kb/genes/$$" 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