b7b9978c92a2376d6d9ef4f0a4974cb8167295f8
gperez2
  Wed Sep 30 14:17:50 2026 -0700
Updating the TAD tracks from the qa-track SKILL.md pass (hg19, hg38, mm10, mm39): shortLabel fixes for cut-off and duplicate ENCODE and 3DGB subtracks, lowercase biosamples in ENCODE longLabels, " bnd" dropped from Schmitt shortLabels, 3DGB subtracks set to pack with three mm10/mm39 defaults turned on, allButtonPair removed so the Schmitt matrix shows, and McArthur item labels hidden. Merged identical description pages into human/ and mouse/, plus description page cleanups (regenerated References, removed the "How to use these tracks" section, ENCODE pages now say 112 of 117 biosamples use Arrowhead). Also updated the ENCODE metadata columns and organ example in the hg38 makedoc. refs #21599

diff --git src/hg/makeDb/trackDb/human/hg19/tad.ra src/hg/makeDb/trackDb/human/hg19/tad.ra
index 83d034ed7f0..73cb2f77abb 100644
--- src/hg/makeDb/trackDb/human/hg19/tad.ra
+++ src/hg/makeDb/trackDb/human/hg19/tad.ra
@@ -1,280 +1,280 @@
 track tads
 superTrack on hide
 shortLabel TADs
 longLabel Topologically associating domains (TADs) and boundaries from Hi-C studies
 group regulation
 html tads
 
 track tadsDixon
 parent tads
 priority 1
 compositeTrack on
 shortLabel Dixon 2012 TADs
 longLabel TAD domains in hESC and IMR90 cells (Dixon et al. 2012, lifted from hg18)
 type bigBed 4
 group regulation
 visibility pack
 html tadsDixon
 
     track tadsDixonHESC
     parent tadsDixon on
     shortLabel hESC TADs
     longLabel TAD domains in H1 human embryonic stem cells (Dixon et al. 2012)
     type bigBed 4
     bigDataUrl /gbdb/$D/bbi/tad/tadsDixonHESC.bb
     color 27,158,119
     mouseOver <b>Cell type:</b> $name (TAD domain)
 
     track tadsDixonIMR90
     parent tadsDixon on
     shortLabel IMR90 TADs
     longLabel TAD domains in IMR90 fetal lung fibroblasts (Dixon et al. 2012)
     type bigBed 4
     bigDataUrl /gbdb/$D/bbi/tad/tadsDixonIMR90.bb
     color 217,95,2
     mouseOver <b>Cell type:</b> $name (TAD domain)
 
 track tadsSchmitt
 parent tads
 priority 2
 compositeTrack on
 shortLabel Schmitt 2016 boundaries
 longLabel TAD boundaries across 21 human tissues and cell lines (Schmitt et al. 2016)
 type bigBed 4
 group regulation
 visibility hide
 html tadsSchmitt
 subGroup1 stype Sample_type cellLine=Cell_line tissue=Primary_tissue
 subGroup2 organ Organ_system brain=Brain cardiovascular=Cardiovascular immune=Immune digestive=Digestive endocrine=Endocrine reproductive=Reproductive muscle=Muscle respiratory=Respiratory urinary=Urinary stem=Stem
 dimensions dimX=organ dimY=stype
 sortOrder stype=+ organ=+
 showSubtrackColorOnUi on
-allButtonPair on
 
     track tadsSchmittGM12878
     parent tadsSchmitt on
-    shortLabel GM12878 bnd
+    shortLabel GM12878
     longLabel TAD boundaries in GM12878 lymphoblastoid cells (Schmitt et al. 2016)
     type bigBed 4
     bigDataUrl /gbdb/$D/bbi/tad/tadsSchmittGM12878.bb
     subGroups stype=cellLine organ=immune
     color 51,160,44
     mouseOver <b>Sample:</b> GM12878 lymphoblastoid cells (TAD boundary, 40 kb bin)
 
     track tadsSchmittH1
     parent tadsSchmitt on
-    shortLabel H1-hESC bnd
+    shortLabel H1-hESC
     longLabel TAD boundaries in H1 human embryonic stem cells (Schmitt et al. 2016)
     type bigBed 4
     bigDataUrl /gbdb/$D/bbi/tad/tadsSchmittH1.bb
     subGroups stype=cellLine organ=stem
     color 152,78,163
     mouseOver <b>Sample:</b> H1 human embryonic stem cells (TAD boundary, 40 kb bin)
 
     track tadsSchmittIMR90
     parent tadsSchmitt on
-    shortLabel IMR90 bnd
+    shortLabel IMR90
     longLabel TAD boundaries in IMR90 fetal lung fibroblasts (Schmitt et al. 2016)
     type bigBed 4
     bigDataUrl /gbdb/$D/bbi/tad/tadsSchmittIMR90.bb
     subGroups stype=cellLine organ=respiratory
     color 178,150,40
     mouseOver <b>Sample:</b> IMR90 fetal lung fibroblasts (TAD boundary, 40 kb bin)
 
     track tadsSchmittMES
     parent tadsSchmitt off
-    shortLabel Mesendoderm bnd
+    shortLabel Mesendoderm
     longLabel TAD boundaries in H1-derived mesendoderm cells (Schmitt et al. 2016)
     type bigBed 4
     bigDataUrl /gbdb/$D/bbi/tad/tadsSchmittMES.bb
     subGroups stype=cellLine organ=stem
     color 152,78,163
     mouseOver <b>Sample:</b> H1-derived mesendoderm cells (TAD boundary, 40 kb bin)
 
     track tadsSchmittMSC
     parent tadsSchmitt off
-    shortLabel Mesench SC bnd
+    shortLabel Mesenchymal SC
     longLabel TAD boundaries in H1-derived mesenchymal stem cells (Schmitt et al. 2016)
     type bigBed 4
     bigDataUrl /gbdb/$D/bbi/tad/tadsSchmittMSC.bb
     subGroups stype=cellLine organ=stem
     color 152,78,163
     mouseOver <b>Sample:</b> H1-derived mesenchymal stem cells (TAD boundary, 40 kb bin)
 
     track tadsSchmittNPC
     parent tadsSchmitt off
-    shortLabel Neural prog bnd
+    shortLabel Neural progenitor
     longLabel TAD boundaries in H1-derived neural progenitor cells (Schmitt et al. 2016)
     type bigBed 4
     bigDataUrl /gbdb/$D/bbi/tad/tadsSchmittNPC.bb
     subGroups stype=cellLine organ=stem
     color 152,78,163
     mouseOver <b>Sample:</b> H1-derived neural progenitor cells (TAD boundary, 40 kb bin)
 
     track tadsSchmittTRO
     parent tadsSchmitt off
-    shortLabel Trophoblast bnd
+    shortLabel Trophoblast
     longLabel TAD boundaries in H1-derived trophoblast-like cells (Schmitt et al. 2016)
     type bigBed 4
     bigDataUrl /gbdb/$D/bbi/tad/tadsSchmittTRO.bb
     subGroups stype=cellLine organ=stem
     color 152,78,163
     mouseOver <b>Sample:</b> H1-derived trophoblast-like cells (TAD boundary, 40 kb bin)
 
     track tadsSchmittAD
     parent tadsSchmitt off
-    shortLabel Adrenal bnd
+    shortLabel Adrenal
     longLabel TAD boundaries in adrenal gland (Schmitt et al. 2016)
     type bigBed 4
     bigDataUrl /gbdb/$D/bbi/tad/tadsSchmittAD.bb
     subGroups stype=tissue organ=endocrine
     color 31,120,180
     mouseOver <b>Sample:</b> adrenal gland (TAD boundary, 40 kb bin)
 
     track tadsSchmittAO
     parent tadsSchmitt off
-    shortLabel Aorta bnd
+    shortLabel Aorta
     longLabel TAD boundaries in aorta (Schmitt et al. 2016)
     type bigBed 4
     bigDataUrl /gbdb/$D/bbi/tad/tadsSchmittAO.bb
     subGroups stype=tissue organ=cardiovascular
     color 227,26,28
     mouseOver <b>Sample:</b> aorta (TAD boundary, 40 kb bin)
 
     track tadsSchmittBL
     parent tadsSchmitt off
-    shortLabel Bladder bnd
+    shortLabel Bladder
     longLabel TAD boundaries in bladder (Schmitt et al. 2016)
     type bigBed 4
     bigDataUrl /gbdb/$D/bbi/tad/tadsSchmittBL.bb
     subGroups stype=tissue organ=urinary
     color 251,154,153
     mouseOver <b>Sample:</b> bladder (TAD boundary, 40 kb bin)
 
     track tadsSchmittCO
     parent tadsSchmitt on
-    shortLabel Cortex bnd
+    shortLabel Cortex
     longLabel TAD boundaries in dorsolateral prefrontal cortex (Schmitt et al. 2016)
     type bigBed 4
     bigDataUrl /gbdb/$D/bbi/tad/tadsSchmittCO.bb
     subGroups stype=tissue organ=brain
     color 106,61,154
     mouseOver <b>Sample:</b> dorsolateral prefrontal cortex (TAD boundary, 40 kb bin)
 
     track tadsSchmittHC
     parent tadsSchmitt off
-    shortLabel Hippocampus bnd
+    shortLabel Hippocampus
     longLabel TAD boundaries in hippocampus (Schmitt et al. 2016)
     type bigBed 4
     bigDataUrl /gbdb/$D/bbi/tad/tadsSchmittHC.bb
     subGroups stype=tissue organ=brain
     color 106,61,154
     mouseOver <b>Sample:</b> hippocampus (TAD boundary, 40 kb bin)
 
     track tadsSchmittLG
     parent tadsSchmitt off
-    shortLabel Lung bnd
+    shortLabel Lung
     longLabel TAD boundaries in lung (Schmitt et al. 2016)
     type bigBed 4
     bigDataUrl /gbdb/$D/bbi/tad/tadsSchmittLG.bb
     subGroups stype=tissue organ=respiratory
     color 178,150,40
     mouseOver <b>Sample:</b> lung (TAD boundary, 40 kb bin)
 
     track tadsSchmittLI
     parent tadsSchmitt on
-    shortLabel Liver bnd
+    shortLabel Liver
     longLabel TAD boundaries in liver (Schmitt et al. 2016)
     type bigBed 4
     bigDataUrl /gbdb/$D/bbi/tad/tadsSchmittLI.bb
     subGroups stype=tissue organ=digestive
     color 255,127,0
     mouseOver <b>Sample:</b> liver (TAD boundary, 40 kb bin)
 
     track tadsSchmittLV
     parent tadsSchmitt off
-    shortLabel Left ventricle bnd
+    shortLabel Left ventricle
     longLabel TAD boundaries in left ventricle of heart (Schmitt et al. 2016)
     type bigBed 4
     bigDataUrl /gbdb/$D/bbi/tad/tadsSchmittLV.bb
     subGroups stype=tissue organ=cardiovascular
     color 227,26,28
     mouseOver <b>Sample:</b> left ventricle of heart (TAD boundary, 40 kb bin)
 
     track tadsSchmittOV
     parent tadsSchmitt off
-    shortLabel Ovary bnd
+    shortLabel Ovary
     longLabel TAD boundaries in ovary (Schmitt et al. 2016)
     type bigBed 4
     bigDataUrl /gbdb/$D/bbi/tad/tadsSchmittOV.bb
     subGroups stype=tissue organ=reproductive
     color 177,89,40
     mouseOver <b>Sample:</b> ovary (TAD boundary, 40 kb bin)
 
     track tadsSchmittPA
     parent tadsSchmitt off
-    shortLabel Pancreas bnd
+    shortLabel Pancreas
     longLabel TAD boundaries in pancreas (Schmitt et al. 2016)
     type bigBed 4
     bigDataUrl /gbdb/$D/bbi/tad/tadsSchmittPA.bb
     subGroups stype=tissue organ=endocrine
     color 31,120,180
     mouseOver <b>Sample:</b> pancreas (TAD boundary, 40 kb bin)
 
     track tadsSchmittPO
     parent tadsSchmitt off
-    shortLabel Psoas muscle bnd
+    shortLabel Psoas muscle
     longLabel TAD boundaries in psoas muscle (Schmitt et al. 2016)
     type bigBed 4
     bigDataUrl /gbdb/$D/bbi/tad/tadsSchmittPO.bb
     subGroups stype=tissue organ=muscle
     color 120,180,200
     mouseOver <b>Sample:</b> psoas muscle (TAD boundary, 40 kb bin)
 
     track tadsSchmittRV
     parent tadsSchmitt off
-    shortLabel Right ventricle bnd
+    shortLabel Right ventricle
     longLabel TAD boundaries in right ventricle of heart (Schmitt et al. 2016)
     type bigBed 4
     bigDataUrl /gbdb/$D/bbi/tad/tadsSchmittRV.bb
     subGroups stype=tissue organ=cardiovascular
     color 227,26,28
     mouseOver <b>Sample:</b> right ventricle of heart (TAD boundary, 40 kb bin)
 
     track tadsSchmittSB
     parent tadsSchmitt off
-    shortLabel Small bowel bnd
+    shortLabel Small bowel
     longLabel TAD boundaries in small bowel (Schmitt et al. 2016)
     type bigBed 4
     bigDataUrl /gbdb/$D/bbi/tad/tadsSchmittSB.bb
     subGroups stype=tissue organ=digestive
     color 255,127,0
     mouseOver <b>Sample:</b> small bowel (TAD boundary, 40 kb bin)
 
     track tadsSchmittSX
     parent tadsSchmitt off
-    shortLabel Spleen bnd
+    shortLabel Spleen
     longLabel TAD boundaries in spleen (Schmitt et al. 2016)
     type bigBed 4
     bigDataUrl /gbdb/$D/bbi/tad/tadsSchmittSX.bb
     subGroups stype=tissue organ=immune
     color 51,160,44
     mouseOver <b>Sample:</b> spleen (TAD boundary, 40 kb bin)
 
 track tadsMcArthur
 parent tads
 priority 3
 shortLabel TAD boundary stability
 longLabel TAD boundary stability across 37 cell-type maps (McArthur & Capra 2021)
 type bigBed 5 + 2
 bigDataUrl /gbdb/$D/bbi/tad/tadsMcArthur.bb
 group regulation
 visibility hide
 spectrum on
 filter.contexts 4:37
 filterByRange.contexts on
 filterLimits.contexts 1:37
-filterLabel.contexts Minimum number of cell-type maps sharing the boundary (1-37)
-mouseOver <b>Boundary recurrent:</b> $contexts / 37 cell-type maps<br><b>Percentile:</b> $percentile
+filterLabel.contexts Number of cell-type maps sharing the boundary
+labelFields none
+mouseOver <b>Boundary recurrent:</b> $contexts / 37 cell-type maps<br><b>Stability percentile (0-1):</b> $percentile
 html tadsMcArthur