9169db807b49113b231d35f2beec4e04c2fb1756
lrnassar
  Wed Jun 3 08:29:02 2026 -0700
Add dataVersion to Orphanet and ClinGen dosage tracks to show upstream release. refs #36455

Orphanet: parse the JDBOR release version (e.g. 1.3.42 / 4.1.8 [2025-03-03]) from
the downloaded XML and write it to a per-assembly version.txt that the orphadata
track points to via dataVersion.

ClinGen: write the ClinGen dosage 'results as of' date (e.g. 28 Apr,2026) from the
curation list header to a version file shared by the clinGenHaplo and clinGenTriplo
subtracks. The other ClinGen feeds publish no dataset-level date, so they are left
unversioned.

The version file is written per assembly only after that assembly's bigBed is
installed, surfacing the source's own release, which can differ from our otto
update timestamp.

diff --git src/hg/makeDb/trackDb/human/trackDb.clinGen.ra src/hg/makeDb/trackDb/human/trackDb.clinGen.ra
index 68aa3949438..b8d6b61864c 100644
--- src/hg/makeDb/trackDb/human/trackDb.clinGen.ra
+++ src/hg/makeDb/trackDb/human/trackDb.clinGen.ra
@@ -1,70 +1,72 @@
 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/$D/bbi/clinGen/clinGenHaplo.bb
+    dataVersion /gbdb/$D/bbi/clinGen/clinGenDosageVersion.txt
     mouseOver <b>Gene/ISCA ID</b>: $name<br> <b>Haploinsufficiency score</b>: $haploScore<br> <b>Dosage Sensitivity Evidence</b>: $haploDescription
     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=$$" mondoID="https://monarchinitiative.org/disease/$$"
 
     track clinGenTriplo
     priority 2
     parent clinGenComp on
     shortLabel ClinGen Triplosensitivity
     longLabel ClinGen Dosage Sensitivity Map - Triplosensitivity
     visibility pack
     type bigBed 9 +
     bigDataUrl /gbdb/$D/bbi/clinGen/clinGenTriplo.bb
+    dataVersion /gbdb/$D/bbi/clinGen/clinGenDosageVersion.txt
     mouseOver <b>Gene/ISCA ID</b>: $name<br> <b>Triplosensitivity score</b>: $triploScore<br> <b>Dosage Sensitivity Evidence</b>: $triploDescription
     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=$$" mondoID="https://monarchinitiative.org/disease/$$"
 
     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
     mouseOver <b>Gene/ISCA ID</b>: $geneSymbol<br> <b>Disease(s)</b>: $name<br> <b>Classification</b>: $Classification
     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