17b7d3c37be41135afaf8e91e365e3847af96ca5
lrnassar
  Mon Jun 22 10:56:56 2026 -0700
Add TAD (topologically associating domains) track set on hg19, hg38, mm10, mm39. refs #21599

New "tads" superTrack collecting published TAD calls, alpha-gated via include tad.ra
alpha in each assembly's trackDb.ra.

hg38 (all five sources): Dixon 2012 domains, Schmitt 2016 boundaries, McArthur & Capra
2021 boundary stability, ENCODE contact domains (faceted composite over 117 biosamples),
and 3D Genome Browser 2.0 domains (faceted composite over 464 datasets).
hg19: the three sources with hg19-compatible data (Dixon, Schmitt, McArthur).
mm10/mm39 (domains only; the boundary sources have no mouse data): Dixon, ENCODE
(faceted, 16 biosamples), and 3D Genome Browser (faceted, 30 datasets); mm39 lifted
from mm10, lift noted in the long labels.

Faceted composites are organ-colored from a TAD-owned organ_colors.json symlinked into
/gbdb/<asm>/bbi/tad/. Build scripts and autoSql are version-controlled under
makeDb/scripts/tad/ and symlinked into the per-source build dirs. Provenance and fetch
for every dataset are documented in the makedocs (doc/hg38/tad.txt, doc/mm10/tad.txt,
doc/mm39/tad.txt, and the hg19 TAD section in doc/hg19.txt).

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+<h2>Description</h2>
+<p>
+This composite shows <b>TAD boundaries</b> across 21 human samples (7 cell lines and 14
+primary tissues) from Schmitt <em>et al.</em>, 2016. A boundary is the insulating region
+that separates two adjacent topologically associating domains. These are
+<em>boundaries</em>, not domains; for domain intervals see the Dixon 2012 TADs track.
+</p>
+<h2>Display Conventions and Configuration</h2>
+<p>
+Each boundary is a 40 kb bin; the bin width reflects the localization precision of the
+40 kb analysis, not a measured physical width. Subtracks are grouped by sample type
+(cell line vs. primary tissue) and organ system, and colored by organ system. Because the
+same boundary is reported independently per sample, turning on multiple subtracks lets you
+read boundary conservation directly: a boundary present in many samples is constitutive,
+while one present in few is cell-type specific. By default a representative subset of
+samples is shown.
+</p>
+<h2>Methods</h2>
+<p>
+Boundaries were called with the insulation-score method at 40 kb resolution (1 Mb
+insulation square, 200 kb delta window) as described in Schmitt <em>et al.</em>, 2016
+(Supplementary Table S3). Per-sample boundary bins were obtained on assembly hg19; for
+this assembly they were used natively or lifted with the UCSC <b>liftOver</b> tool, with a
+small fraction of bins that did not map cleanly dropped.
+</p>
+
+<h2>Data Access</h2>
+<p>
+The raw data can be explored interactively with the
+<a href="hgTables" target="_blank">Table Browser</a> or the
+<a href="hgIntegrator" target="_blank">Data Integrator</a>. For programmatic access, the
+track can be accessed using the Genome Browser's
+<a href="https://genome.ucsc.edu/goldenPath/help/api.html" target="_blank">REST API</a>.
+The underlying bigBed files can be downloaded from our
+<a href="https://hgdownload.soe.ucsc.edu/gbdb/$db/bbi/tad/" target="_blank">download server</a>.
+</p>
+
+<h2>References</h2>
+<p>
+Schmitt AD, Hu M, Jung I, Xu Z, Qiu Y, Tan CL, Li Y, Lin S, Lin Y, Barr CL, Ren B.
+A Compendium of Chromatin Contact Maps Reveals Spatially Active Regions in the Human
+Genome. <em>Cell Rep</em>. 2016;17(8):2042-2059.
+<a href="https://doi.org/10.1016/j.celrep.2016.10.061" target="_blank">doi:10.1016/j.celrep.2016.10.061</a>
+</p>