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/doc/hg38/tad.txt src/hg/makeDb/doc/hg38/tad.txt
index 77e586ac84b..a4a209ab73e 100644
--- src/hg/makeDb/doc/hg38/tad.txt
+++ src/hg/makeDb/doc/hg38/tad.txt
@@ -114,38 +114,38 @@
 # this drops loop files), normalize chrom to "chr*" and validate against chrom.sizes; map
 # bedpe cols to bed4+5 (chrom, x1, x2, biosample, cornerScore=col12, uVarScore=13, lVarScore=14,
 # upSign=15, loSign=16); merge replicate domains whose endpoints both fall within one 5 kb bin,
 # keeping the higher cornerScore (scores taken verbatim, never blended -- verified against the
 # retired tadsEncodeGM12878.bb). autoSql = /hive/data/outside/tad/tadDomainEncode.as.
 # Facet metadata (organ_slims, classification, life_stage) fetched once from the ENCODE REST API
 # for all 228 candidate experiments -> source/encode_meta_all.json; perturbed flag ->
 # source/encode_perturbed.json. organ_slims (lowercase, multi-valued) mapped to organ_colors.json
 # keys and reduced to one organ per biosample by an anatomical-specificity priority (Blood vessel
 # and Muscle rank above Limb/Placenta so HUVEC->Blood vessel, tibial artery->Blood vessel,
 # gastrocnemius->Muscle); 4 biosamples with empty organ_slims assigned by known biology.
 # primaryKey = the chosen experiment Accession (ENCSR), linked to the ENCODE portal via
 # subtrackUrls (like wgEncodeReg4); the readable biosample name (_Biosample) and full ENCODE
 # summary (_Description) are shown in the metadata table but not faceted. shortLabels are
 # word-boundary summaries (no mid-word truncation; CD4-positive->CD4+ etc.); bigBed filenames
-# keep the readable biosample symbol. (A549 organ "musculature of body"->Muscle and similar
-# follow ENCODE's organ_slim verbatim; organ reflects ENCODE's annotation, not a disease-origin call.)
+# keep the readable biosample symbol. (Organ is ENCODE's organ_slim annotation, not our own call
+# on where a cancer cell line came from, e.g. A673 "musculature of body" -> Muscle.)
 
 cd /hive/data/outside/tad/encode/build
 python3 buildTadsEncode.py
 # -> hg38/tadsEncode/<symbol>.bb  (117 bigBeds, bigBed 4+5)
-# -> hg38/tadsEncode_metadata.tsv (118 rows; cols Biosample Organ Biosample_type Assay
-#    Life_stage Calls _Biosample)
+# -> hg38/tadsEncode_metadata.tsv (118 rows; cols Accession _Biosample Organ Biosample_type
+#    Assay Life_stage Calls _Description)
 # -> hg38/tadsEncode.ra  (faceted composite header + 117 subtrack stanzas)
 
 # Symlink bigBeds (directory symlink) and metadata TSV into /gbdb
 cd /gbdb/hg38/bbi/tad
 ln -sfn /hive/data/outside/tad/encode/build/hg38/tadsEncode tadsEncode
 ln -sfn /hive/data/outside/tad/encode/build/hg38/tadsEncode_metadata.tsv tadsEncode_metadata.tsv
 
 # trackDb: the old inline tadsEncode composite in tad.ra was replaced by:  include tadsEncode.ra
 #   ~/kent/src/hg/makeDb/trackDb/human/hg38/tadsEncode.ra   (composite + 117 subtracks)
 #   ~/kent/src/hg/makeDb/trackDb/human/hg38/tadsEncode.html (description page)
 cp /hive/data/outside/tad/encode/build/hg38/tadsEncode.ra \
    ~/kent/src/hg/makeDb/trackDb/human/hg38/tadsEncode.ra
 
 cd ~/kent/src/hg/makeDb/trackDb
 make DBS=hg38 FIND=find