d033cea2063e9362949baf5b4d8b837597173a0d
max
Thu Sep 10 05:16:05 2026 -0700
Address the code review of the Sep 9 commits
Faceted composite: text that comes from a hub - a metadata column's
description, the name and title of a data type, and the values quoted back in
the "could not load the metadata" row - is put on the page as text rather than
as markup. The three places built their markup from template strings, so a
value carrying angle brackets or a quote was read as HTML: the column
description now goes through the shared htmlEncode() once where the header is
parsed, and the other two build their elements as nodes. The error row reads
better for it as well, since a value with brackets in it used to disappear from
the message that was meant to show it.
The saved UI state keys on the assembly as well as the metadata id. localStorage
is per-origin, so two assemblies whose tracks share a name were sharing one
entry, and a row order dragged on one came back on the other over a different
set of samples. hgTrackUi passes the database down for it. State saved under the
old key is dropped, which costs a facet selection or a page length.
Imprinting: the five subtrack description pages link back to the container as
hgTrackUi?db=$db&g=$parentTrack, without the hgsid. Native trackDb html is
substituted by hgTrackDb as it loads the table, where there is no cart, so
${hgsid} came out empty and the link read 'hgsid=&g=...'. Matches what the
Fiber-seq pages already do. The makeDoc note that described the old form is
updated with the reason.
UniProt otto: README.txt lists all eight things that reach runLog.txt. It had
four, and was missing LOCKED, along with PREFLIGHT-FAIL, END and INTERRUPTED.
refs #36210
refs #37599
refs #38300
diff --git src/hg/makeDb/trackDb/human/hg38/omimImprint.html src/hg/makeDb/trackDb/human/hg38/omimImprint.html
index f7715271866..c594a2201a3 100644
--- src/hg/makeDb/trackDb/human/hg38/omimImprint.html
+++ src/hg/makeDb/trackDb/human/hg38/omimImprint.html
@@ -1,152 +1,152 @@
<h2>Description</h2>
<p>
-Part of the <a href="hgTrackUi?db=$db&hgsid=${hgsid}&g=$parentTrack">Imprinting</a> track collection, this track shows the genes that OMIM, the catalog of
+Part of the <a href="hgTrackUi?db=$db&g=$parentTrack">Imprinting</a> track collection, this track shows the genes that OMIM, the catalog of
human genes and genetic disorders curated at Johns Hopkins, marks as imprinted or candidate
imprinted. The OMIM staff assign that mark by reading the primary literature. It is published only through
<a href="https://genescout.omim.org/" target="_blank">GeneScout</a>, OMIM's tool
for listing the genes and phenotypes inside a set of genomic intervals, which
appends <tt>(I)</tt> to the coordinates of a flagged gene in its Location
column. The mark is not part of the OMIM gene map and does not appear in any of
the OMIM download files. Because the set is curated by hand it is smaller than
the computational predictions in the other tracks of this collection, and it is
tied directly to the OMIM entries for each gene.
</p>
<p>
The OMIM curators point out that the flag covers both genes where imprinting is
established and genes where it is still only a candidate, and that the export
does not say which is which. A gene in this track is therefore a pointer into
its OMIM entry rather than a settled call.
</p>
<p>
The track holds 459 loci. Of these, 225 have an OMIM gene entry of their own
and 234 appear in the gene map without one; the second group is mostly
antisense transcripts, long non-coding RNAs and microRNAs sitting inside
imprinted clusters, such as KCNQ1-AS1 and INS-IGF2.
</p>
<h2>Display Conventions and Configuration</h2>
<p>
Each item is one OMIM gene entry, drawn over the gene span that OMIM gives.
OMIM does not report a strand, so the items are drawn without one. Clicking an
item opens a page with the MIM number, the full gene name, the other symbols
OMIM lists for the locus, and every OMIM phenotype associated with the gene.
The gene symbol links to the OMIM entry.
</p>
<p>
OMIM records that a gene is imprinted or a candidate, but not which parental copy is active, so
every item here is drawn in the neutral gray that this collection uses for
annotations without a parent of origin. Vermillion and blue keep their meaning
on the other subtracks: the maternal and the paternal copy.
</p>
<table class="stdTbl">
<tr><th style="background-color:#555555;width:2em"> </th>
<td>Gray — imprinted or candidate imprinted according to OMIM, parental copy
not stated</td></tr>
</table>
<p>
Methylation itself is annotated elsewhere. The Kaplan lab human methylation
atlas is a separate track,
<a href="hgTrackUi?g=humanMethylationAtlasSummary">Human Methylation Atlas
Summary</a>, under DNA Methylation.
</p>
<p>
A filter separates the genes that have an OMIM gene entry of their own from the
loci that appear in the gene map without one, which are mostly antisense
transcripts and other non-coding genes at imprinted clusters. It does not
filter anything out by default.
</p>
<h2>Methods</h2>
<p>
OMIM curators read the primary literature and record, for each gene, the
phenotypes it causes, the mode of inheritance and a set of annotations, one of
which is that the gene is imprinted or a candidate for it. That annotation surfaces only in GeneScout
output, where it is appended as <tt>(I)</tt> to the coordinates in the Location
column; it is in neither the OMIM gene map nor the OMIM download files.
GeneScout is described in Applegate et al. (2022).
</p>
<p>
The gene list was exported from
<a href="https://genescout.omim.org/" target="_blank">GeneScout</a> as a
tab-delimited file, using a search that covers every chromosome on assembly
GRCh38, and the flagged entries were converted to browser coordinates. GeneScout
also lists OMIM phenotype entries alongside genes; those are mapped disease
regions rather than gene positions, some of them tens of megabases long, so they
are not shown here. The Genome Browser already has them in the
<a href="hgTrackUi?g=omimLocation">OMIM Cyto Loci</a> track. The processing
steps are documented in the
<a href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/doc/hg38/imprinting.txt" target="_blank">imprinting makeDoc</a>
and the script is in
<a href="https://github.com/ucscGenomeBrowser/kent/tree/master/src/hg/makeDb/scripts/imprinting" target="_blank">makeDb/scripts/imprinting</a>.
</p>
<h2>Data Access</h2>
<p>
The data can be explored interactively in table format with the
<a href="../cgi-bin/hgTables">Table Browser</a> or the
<a href="../cgi-bin/hgIntegrator">Data Integrator</a> and exported from there to
spreadsheet or tab-sep tables. From scripts, the data can be accessed through
our <a href="https://api.genome.ucsc.edu">API</a>, track=<i>omimImprint</i>.
</p>
<p>
For automated download and analysis, the genome annotation is stored in a
bigBed file that can be downloaded from
<a href="http://hgdownload.soe.ucsc.edu/gbdb/hg38/imprinting/omimImprint/" target="_blank">our download server</a>.
The file for this track is called <tt>omimImprint.bb</tt>. Individual regions or
the whole genome annotation can be obtained using our tool
<tt>bigBedToBed</tt>, which can be compiled from the source code or downloaded
as a precompiled binary for your system. Instructions for downloading source
code and binaries can be found
<a href="http://hgdownload.soe.ucsc.edu/downloads.html#utilities_downloads">here</a>.
The tool can also be used to obtain features within a given range, e.g.
<tt>bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/hg38/imprinting/omimImprint/omimImprint.bb -chrom=chr15 -start=23000000 -end=26000000 stdout</tt>
</p>
<p>
The original gene list can be exported from
<a href="https://genescout.omim.org/" target="_blank">GeneScout</a>. Use of OMIM
resources requires agreement to the
<a href="https://omim.org/help/agreement" target="_blank">OMIM terms of use</a>.
</p>
<h2>Credits</h2>
<p>
Thanks to the OMIM curators at the McKusick-Nathans Institute of Genetic
Medicine, Johns Hopkins University School of Medicine, for maintaining the
catalog, and in particular to Joanna Amberger for explaining how to export the
gene list from GeneScout.
</p>
<h2>References</h2>
<p>
Applegate CD, Schiettecatte F, Hamosh A, Amberger JS.
<a href="https://doi.org/10.1002/cpz1.530" target="_blank">
Exploring Genes and Phenotypes Within Chromosomal Regions Using OMIM's GeneScout</a>.
<em>Curr Protoc</em>. 2022 Sep;2(9):e530.
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/36130039" target="_blank">36130039</a>
</p>
<p>
Amberger JS, Bocchini CA, Schiettecatte F, Scott AF, Hamosh A.
<a href="https://www.ncbi.nlm.nih.gov/pubmed/25428349" target="_blank">
OMIM.org: Online Mendelian Inheritance in Man (OMIM®), an online catalog of human genes and genetic
disorders</a>.
<em>Nucleic Acids Res</em>. 2015 Jan;43(Database issue):D789-98.
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/25428349" target="_blank">25428349</a>; PMC: <a
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4383985/" target="_blank">PMC4383985</a>
</p>