691a2b8981d6db69e8707ea44041c4661cdac97e
max
  Wed Sep 9 06:38:29 2026 -0700
Imprinting: add the ASM Atlas tracks, and tidy the collection's labels

Adds a composite built from Rosenski et al. 2025, "Atlas of imprinted and
allele-specific DNA methylation in the human body". Three subtracks: the
458 regions whose methylation follows the parent of origin, the 72 known
control regions with the boundaries the paper redrew, and the pool of
385,235 regions carrying two methylation states that those came out of.
A fourth set, the regions whose methylation follows a nearby SNP, is
built by the scripts but its stanza is commented out, since sequence
driven methylation is not imprinting.

The authors released hg19 only, so all three are lifted. Their published
files are close to bare BED, so the SNPs, cell types, p-values, gene
links and gamete methylation on the details pages are read out of the
paper's supplementary tables and joined on by position. Regions that
lift but change length by more than 10%, because hg38 added sequence
inside them, are kept with a note rather than dropped: one of them is
TCEB3C, the only control region on chr18.

Also across the collection:
- long labels name their source right after "Imprinting", so that a
label read on its own says where the data came from
- the two gene catalogs are worded alike, and ordered OMIM, Geneimprint,
MethBase2, Akbari, ASM Atlas
- the OMIM curators confirmed that their (I) marker covers established
and candidate imprinted genes alike, with nothing in the export to
tell them apart. Labels, description page and makeDoc now say so, and
the claim that the set is "more conservative" than the computational
tracks is gone. The bigBed was rebuilt for the autoSql line, same 459
features.
- every subtrack page opens by naming the collection, linked back to
its hgTrackUi page, and no longer repeats the collection page's
introduction to imprinting

refs #37599

diff --git src/hg/makeDb/scripts/imprinting/omimImprint.as src/hg/makeDb/scripts/imprinting/omimImprint.as
index 16d84241460..0edc4ed000f 100644
--- src/hg/makeDb/scripts/imprinting/omimImprint.as
+++ src/hg/makeDb/scripts/imprinting/omimImprint.as
@@ -1,17 +1,17 @@
 table omimImprint
-"Genes curated as imprinted by OMIM, from a GeneScout export"
+"Genes curated as imprinted or candidate imprinted by OMIM, from a GeneScout export"
     (
     string chrom;         "Chromosome (or contig, scaffold, etc.)"
     uint   chromStart;    "Start position in chromosome"
     uint   chromEnd;      "End position in chromosome"
     string name;          "Gene symbol"
     uint   score;         "Score (unused, always 0)"
     char[1] strand;       "Strand, not given by OMIM, always ."
     uint   thickStart;    "Start of thick display"
     uint   thickEnd;      "End of thick display"
     uint   reserved;      "Color, neutral gray, see the description page"
     string mimNumber;     "MIM Number|OMIM identifier of the gene entry, empty when the gene has none"
     string cytoLocation;  "Cytogenetic Location|Band as given by OMIM"
     lstring geneName;     "Gene Name|Full gene name"
     string entryType;     "Entry Type|Whether OMIM has a gene entry for this locus"
     lstring phenotypes;   "Phenotypes|OMIM phenotypes listed alongside this gene in the export"